I'm having the exact same problem. I've taken the following steps so far:
- Deleted chrome user settings
- Uninstalled Chrome
- Updated nVidia driver (clean install)
- Reinstalled Chrome

Here is my basic system profile:

Item	Value	
OS Name	Microsoft Windows 10 Pro	
Version	10.0.14393 Build 14393	
Other OS Description 	Not Available	
OS Manufacturer	Microsoft Corporation	
System Name	GLENN-LENOVO-P7	
System Manufacturer	LENOVO	
System Model	20ERCTO1WW	
System Type	x64-based PC	
System SKU	LENOVO_MT_20ER_BU_Think_FM_ThinkPad P70	
Processor	Intel(R) Xeon(R) CPU E3-1505M v5 @ 2.80GHz, 2808 Mhz, 4 Core(s), 8 Logical Processor(s)	
BIOS Version/Date	LENOVO N1DET77W (2.08 ), 8/3/2016	
SMBIOS Version	2.8	
Embedded Controller Version	1.15	
BIOS Mode	UEFI	
BaseBoard Manufacturer	LENOVO	
BaseBoard Model	Not Available	
BaseBoard Name	Base Board	
Platform Role	Mobile	
Secure Boot State	On	
PCR7 Configuration	Elevation Required to View	
Windows Directory	C:\WINDOWS	
System Directory	C:\WINDOWS\system32	
Boot Device	\Device\HarddiskVolume1	
Locale	United States	
Hardware Abstraction Layer	Version = "10.0.14393.206"	
User Name	GLENN-LENOVO-P7\Glenn	
Time Zone	Central Daylight Time	
Installed Physical Memory (RAM)	64.0 GB	
Total Physical Memory	63.8 GB	
Available Physical Memory	57.8 GB	
Total Virtual Memory	95.8 GB	
Available Virtual Memory	89.4 GB	
Page File Space	32.0 GB	
Page File	C:\pagefile.sys	
Hyper-V - VM Monitor Mode Extensions	Yes	
Hyper-V - Second Level Address Translation Extensions	Yes	
Hyper-V - Virtualization Enabled in Firmware	Yes	
Hyper-V - Data Execution Protection	Yes	

I have the same issue. Tried the same steps as above. Primary monitor is 175% scaling 3840 × 2160. Secondary monitor is 100% scaling 1920 x 1080 in portrait orientation.

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	screenshot_from_24_inch_1920_monitor.JPG 80.0 KB View Download

To add to my above comment, this problem only occurs when my secondary monitor is set to 100% scaling in windows 10. If I set the second monitor to 125% the problem disappears but then everything is too large for my taste.

Same issue. Primary monitor is 3840 x 2160, set to 175% scaling. Secondary monitor is 1920 x 1080 set to 100%. On this secondary monitor, the top of the window is cut off, buttons are too big.

Possibly related, all non-maximized Chrome windows seem to have an oversize title bar on the secondary screen. See screenshot, compare to Windows Task Manager title bar. The "Save file" window is incorrectly scaled as well. See screenshot.

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	3aea7f1d535268d90e6cf125b6267dfd.png 399 KB View Download

Seems to be the same issue I reported there : https://bugs.chromium.org/p/chromium/issues/detail?id=643588

Same issue with 55.0.2883.75 (Official Build) m (64-bit)

Primary is 200%, secondary is 100% scaling. At 150% and 175% scaling on secondary it appears as expected, but exhibits this defect at 100% and 125%

As per comment #5 merging this issue in to  bug 643588 , Please feel free to undupe if it's a different one.

Thanks!