Handbrake hangs at 100%

I wanted to convert one of my exercise DVD discs (VIDEO_TS folder) to mp4 but for some reason, Handbrakes always hung at 100% and the file kept growing. The activity window showed the following:

[14:12:47] sync: adding 252 ms of silence to audio 0 start 15879500, next 15856782
[14:12:47] sync: adding 307 ms of silence to audio 0 start 16039772, next 16012100
[14:12:47] sync: audio 0 time went backwards 0 ms, dropped 25 frames (next 16040900, current 16040900)
[14:12:53] sync: adding 70 ms of silence to audio 0 start 19398884, next 19392572
[14:12:58] sync: adding 70 ms of silence to audio 0 start 22515044, next 22508732
[14:13:03] sync: adding 70 ms of silence to audio 0 start 25631204, next 25624892

After using Ctrl+C to kill the process, the resulting file only has the first two chapters, the rest of it consisted the repeats of a couple of frames.

I used Magic DVD copier to cut down the DVD content to only the title with the chapters I want. But Handbrake still hung at 100%.

Finally I concatenated the VOBs (there are three, copy /b file1+file2+file3 big_file) in the folder and converted it. Finally, it was a success.

Looks like the problem is something to do with the wrong Chaptering and sync. Handbrake just couldn't handle it. And it can do it if it's pure vob files. Still a mystery to me...