Here is my about:gpu with hardware acceleration turned on:

Graphics Feature Status
Canvas: Hardware accelerated
Flash: Hardware accelerated
Flash Stage3D: Hardware accelerated
Flash Stage3D Baseline profile: Hardware accelerated
Compositing: Hardware accelerated
Multiple Raster Threads: Enabled
Native GpuMemoryBuffers: Software only. Hardware acceleration disabled
Rasterization: Software only. Hardware acceleration disabled
Video Decode: Software only, hardware acceleration unavailable
Video Encode: Hardware accelerated
VPx Video Decode: Software only, hardware acceleration unavailable
WebGL: Hardware accelerated
WebGL2: Hardware accelerated
Driver Bug Workarounds
adjust_src_dst_region_for_blitframebuffer
clear_uniforms_before_first_program_use
count_all_in_varyings_packing
decode_encode_srgb_for_generatemipmap
disable_framebuffer_cmaa
disable_post_sub_buffers_for_onscreen_surfaces
msaa_is_slow
scalarize_vec_and_mat_constructor_args
Problems Detected
Accelerated video decode is unavailable on Linux: 137247
Disabled Features: accelerated_video_decode
Clear uniforms before first program use on all platforms: 124764, 349137
Applied Workarounds: clear_uniforms_before_first_program_use
Mesa drivers in Linux handle varyings without static use incorrectly: 333885
Applied Workarounds: count_all_in_varyings_packing
Disable partial swaps on Mesa drivers (detected with GL_RENDERER): 339493
Applied Workarounds: disable_post_sub_buffers_for_onscreen_surfaces
Always rewrite vec/mat constructors to be consistent: 398694
Applied Workarounds: scalarize_vec_and_mat_constructor_args
On Intel GPUs MSAA performance is not acceptable for GPU rasterization: 527565
Applied Workarounds: msaa_is_slow
Timer queries crash on Intel GPUs on Linux: 540543, 576991
Limited enabling of Chromium GL_INTEL_framebuffer_CMAA: 535198
Applied Workarounds: disable_framebuffer_cmaa
Disable partial swaps on Mesa drivers (detected with GL_VERSION): 339493
Applied Workarounds: disable_post_sub_buffers_for_onscreen_surfaces
Decode and encode before generateMipmap for srgb format textures on os except macosx: 634519
Applied Workarounds: decode_encode_srgb_for_generatemipmap
adjust src/dst region if blitting pixels outside read framebuffer on Linux Intel: 664740
Applied Workarounds: adjust_src_dst_region_for_blitframebuffer
Disable KHR_blend_equation_advanced until cc shaders are updated: 661715
Accelerated rasterization has been disabled, either via blacklist, about:flags or the command line.
Disabled Features: rasterization
Native GpuMemoryBuffers have been disabled, either via about:flags or command line.
Disabled Features: native_gpu_memory_buffers
Version Information
Data exported	1/20/2017, 11:44:44 PM
Chrome version	Chrome/57.0.2986.0
Operating system	Linux 4.4.0-21-generic
Software rendering list version	12.09
Driver bug list version	9.28
ANGLE commit id	fd8b469ebc8f
2D graphics backend	Skia/57 412a86d014783be99a7a9a0fae407791b95806e8
Command Line Args	--user-data-dir=/home/akalin/.config/google-chrome-unstable --user-data-dir=/home/akalin/.config/google-chrome-unstable --flag-switches-begin --flag-switches-end
Driver Information
Initialization time	26
In-process GPU	false
Passthrough Command Decoder	false
Sandboxed	true
GPU0	VENDOR = 0x8086, DEVICE= 0x1926
Optimus	false
AMD switchable	false
Driver vendor	Mesa
Driver version	12.0.3
Driver date	
Pixel shader version	4.30
Vertex shader version	4.30
Max. MSAA samples	16
Machine model name	
Machine model version	
GL_VENDOR	Intel Open Source Technology Center
GL_RENDERER	Mesa DRI Intel(R) Iris Graphics 540 (Skylake GT3e)
GL_VERSION	4.3 (Core Profile) Mesa 12.0.3
GL_EXTENSIONS	GL_3DFX_texture_compression_FXT1 GL_AMD_conservative_depth GL_AMD_draw_buffers_blend GL_AMD_seamless_cubemap_per_texture GL_AMD_shader_stencil_export GL_AMD_shader_trinary_minmax GL_AMD_vertex_shader_layer GL_AMD_vertex_shader_viewport_index GL_ANGLE_texture_compression_dxt3 GL_ANGLE_texture_compression_dxt5 GL_APPLE_object_purgeable GL_ARB_ES2_compatibility GL_ARB_ES3_compatibility GL_ARB_arrays_of_arrays GL_ARB_base_instance GL_ARB_blend_func_extended GL_ARB_buffer_storage GL_ARB_clear_buffer_object GL_ARB_clear_texture GL_ARB_clip_control GL_ARB_compressed_texture_pixel_storage GL_ARB_compute_shader GL_ARB_conditional_render_inverted GL_ARB_conservative_depth GL_ARB_copy_buffer GL_ARB_copy_image GL_ARB_cull_distance GL_ARB_debug_output GL_ARB_depth_buffer_float GL_ARB_depth_clamp GL_ARB_derivative_control GL_ARB_direct_state_access GL_ARB_draw_buffers GL_ARB_draw_buffers_blend GL_ARB_draw_elements_base_vertex GL_ARB_draw_indirect GL_ARB_draw_instanced GL_ARB_explicit_attrib_location GL_ARB_explicit_uniform_location GL_ARB_fragment_coord_conventions GL_ARB_fragment_layer_viewport GL_ARB_fragment_shader GL_ARB_framebuffer_no_attachments GL_ARB_framebuffer_object GL_ARB_framebuffer_sRGB GL_ARB_get_program_binary GL_ARB_get_texture_sub_image GL_ARB_gpu_shader5 GL_ARB_gpu_shader_fp64 GL_ARB_half_float_pixel GL_ARB_half_float_vertex GL_ARB_instanced_arrays GL_ARB_internalformat_query GL_ARB_internalformat_query2 GL_ARB_invalidate_subdata GL_ARB_map_buffer_alignment GL_ARB_map_buffer_range GL_ARB_multi_bind GL_ARB_multi_draw_indirect GL_ARB_occlusion_query2 GL_ARB_pipeline_statistics_query GL_ARB_pixel_buffer_object GL_ARB_point_sprite GL_ARB_program_interface_query GL_ARB_provoking_vertex GL_ARB_query_buffer_object GL_ARB_robust_buffer_access_behavior GL_ARB_robustness GL_ARB_sample_shading GL_ARB_sampler_objects GL_ARB_seamless_cube_map GL_ARB_seamless_cubemap_per_texture GL_ARB_separate_shader_objects GL_ARB_shader_atomic_counters GL_ARB_shader_bit_encoding GL_ARB_shader_clock GL_ARB_shader_draw_parameters GL_ARB_shader_image_load_store GL_ARB_shader_image_size GL_ARB_shader_objects GL_ARB_shader_precision GL_ARB_shader_stencil_export GL_ARB_shader_storage_buffer_object GL_ARB_shader_subroutine GL_ARB_shader_texture_image_samples GL_ARB_shader_texture_lod GL_ARB_shading_language_420pack GL_ARB_shading_language_packing GL_ARB_stencil_texturing GL_ARB_sync GL_ARB_tessellation_shader GL_ARB_texture_barrier GL_ARB_texture_buffer_object GL_ARB_texture_buffer_object_rgb32 GL_ARB_texture_buffer_range GL_ARB_texture_compression_bptc GL_ARB_texture_compression_rgtc GL_ARB_texture_cube_map_array GL_ARB_texture_float GL_ARB_texture_gather GL_ARB_texture_mirror_clamp_to_edge GL_ARB_texture_multisample GL_ARB_texture_non_power_of_two GL_ARB_texture_query_levels GL_ARB_texture_query_lod GL_ARB_texture_rectangle GL_ARB_texture_rg GL_ARB_texture_rgb10_a2ui GL_ARB_texture_stencil8 GL_ARB_texture_storage GL_ARB_texture_storage_multisample GL_ARB_texture_swizzle GL_ARB_texture_view GL_ARB_transform_feedback2 GL_ARB_transform_feedback3 GL_ARB_transform_feedback_instanced GL_ARB_uniform_buffer_object GL_ARB_vertex_array_bgra GL_ARB_vertex_array_object GL_ARB_vertex_attrib_64bit GL_ARB_vertex_attrib_binding GL_ARB_vertex_shader GL_ARB_vertex_type_10f_11f_11f_rev GL_ARB_vertex_type_2_10_10_10_rev GL_ARB_viewport_array GL_ATI_blend_equation_separate GL_ATI_texture_float GL_EXT_abgr GL_EXT_blend_equation_separate GL_EXT_draw_buffers2 GL_EXT_draw_instanced GL_EXT_framebuffer_blit GL_EXT_framebuffer_multisample GL_EXT_framebuffer_multisample_blit_scaled GL_EXT_framebuffer_sRGB GL_EXT_packed_depth_stencil GL_EXT_packed_float GL_EXT_pixel_buffer_object GL_EXT_polygon_offset_clamp GL_EXT_provoking_vertex GL_EXT_shader_integer_mix GL_EXT_shader_samples_identical GL_EXT_texture_array GL_EXT_texture_compression_dxt1 GL_EXT_texture_compression_rgtc GL_EXT_texture_compression_s3tc GL_EXT_texture_filter_anisotropic GL_EXT_texture_integer GL_EXT_texture_sRGB GL_EXT_texture_sRGB_decode GL_EXT_texture_shared_exponent GL_EXT_texture_snorm GL_EXT_texture_swizzle GL_EXT_transform_feedback GL_EXT_vertex_array_bgra GL_IBM_multimode_draw_arrays GL_KHR_context_flush_control GL_KHR_debug GL_KHR_robust_buffer_access_behavior GL_KHR_robustness GL_KHR_texture_compression_astc_ldr GL_MESA_pack_invert GL_MESA_texture_signed_rgba GL_NV_conditional_render GL_NV_depth_clamp GL_NV_packed_depth_stencil GL_NV_texture_barrier GL_OES_EGL_image GL_OES_read_format GL_S3_s3tc
Disabled Extensions	GL_ARB_timer_query GL_EXT_timer_query GL_KHR_blend_equation_advanced GL_KHR_blend_equation_advanced_coherent
Window system binding vendor	SGI
Window system binding version	1.4
Window system binding extensions	GLX_ARB_create_context GLX_ARB_create_context_profile GLX_ARB_create_context_robustness GLX_ARB_fbconfig_float GLX_ARB_framebuffer_sRGB GLX_ARB_multisample GLX_EXT_create_context_es_profile GLX_EXT_create_context_es2_profile GLX_EXT_fbconfig_packed_float GLX_EXT_framebuffer_sRGB GLX_EXT_import_context GLX_EXT_texture_from_pixmap GLX_EXT_visual_info GLX_EXT_visual_rating GLX_MESA_copy_sub_buffer GLX_OML_swap_method GLX_SGI_swap_control GLX_SGIS_multisample GLX_SGIX_fbconfig GLX_SGIX_pbuffer GLX_SGIX_visual_select_group GLX_INTEL_swap_event
Window manager	Compiz
XDG_CURRENT_DESKTOP	Unity
GDMSESSION	ubuntu
Compositing manager	Yes
Direct rendering	Yes
Reset notification strategy	0x8252
GPU process crash count	0
System visual ID	33
RGBA visual ID	120
Compositor Information
Tile Update Mode	One-copy
Partial Raster	Enabled
GpuMemoryBuffers Status
ATC	Software only
ATCIA	Software only
DXT1	Software only
DXT5	Software only
ETC1	Software only
R_8	Software only
RG_88	Software only
BGR_565	Software only
RGBA_4444	Software only
RGBX_8888	Software only
RGBA_8888	Software only
BGRX_8888	Software only
BGRA_8888	Software only
YVU_420	Software only
YUV_420_BIPLANAR	Software only
UYVY_422	Software only

BTW, chrome version after restart is Version 57.0.2986.0 dev (64-bit) . Although this problem has been present for some time (months) now.

Anything I can do to help investigate this?

Suspect this is driver- or Unity-related.

piman@: is there anything Chrome can do here, or is this up to the driver?

This machine is the Intel NUC6i5SYK, with GPU Intel Iris Graphics 540 (Skylake-U GT3e). I'm using Ubuntu 16.10. Looks like there's this: https://01.org/linuxgraphics/downloads/intel-graphics-update-tool-linux-os-v2.0.4 , which I'll try.

Upgraded driver, turned GPU accel back on, still can repro. Sigh. When I have time, I'll try a non-Unity WM.

Upgraded to Ubuntu Zesty, still same problem.

I narrowed down what triggers the slowness though -- if I have a youtube tab open playing a movie, then the other window becomes slow. If I close it, then it comes back to normal speed.

+sunnyps
Is this the same as  bug 528803 ?

Having a tab with an animated gif seems to trigger it too! But only if it's the foreground tab in one window.

Also, moving the second window to the same desktop as the first window stops it, even with the animated gif in the foreground window of the first.

So seems related...

#9: The general issue of frame rate being divided when multiple windows try to animate irrespective of workspaces is a Chrome issue.

But I didn't think moving from one workspace to another would have an effect. At least it doesn't without any compositing manager. I'll try out Unity and Cinnamon later today.

fwiw I have a patch that fixes this for nvidia: https://chromium-review.googlesource.com/c/479566/

sunnyps@ assigning to you per comment #12.