I agree, autosizing is 100% the problem. I've loaded subtitles int BDSup2Sub and output them supposedly unchanged... and it has the jitter.
Frankly, I'm not even sure it is a needed step, but there is definitely something wrong with the method used.
If you have an idea on how they can fix it, I urge you to go to the Doom9 thread where they're working on this and help them out.