Chrome OS Version: 
R68-10654.0.0

Repro steps:
1. Use VAAPI to encode JPEG image. 
2. Provide a VAEncPackedHeaderDataBufferType with a header containing APP1 segment which has a thumbnail.
3. The resulted JPEG is extremely small, containing only the APP1 segment until end-of-image marker (0xFFD9) of the thumbnail.

My guess is that the end-of-image marker of the thumbnail confuses the VAAPI encoder. If I provide an all-zero APP1 segment with the same size and fill in the real APP1 segment after obtaining the result image from VAAPI, the image looks good.