mkv2vob subtitle timing problem

[HeroSmero]

I've been using mkv2vop to convert some files to play on my ps3 and I've had issues with the subtitle timing being off occasionally. When I convert a number of episodes of a show, sometimes one or two episodes will have subtitles that are somewhat off from the audio/video and occasionally every episodes of a show I'm converting will have mistimed subtitles. My settings in the configuration are as follows:

Output type: File
Preferred Audio Language: Japanese
Video Transcoding: Auto
Preferred Subtitle Language: English
File Splitting: None
Output File Extension: Auto
Transcoding Codec: x256(slow)

Always Transcode Subtitles: Checked
Large Subtitles: Checked
Always Transcode DTS: Checked
Automatic Update: Checked

Also, I've been converting my files to an external harddrive (in case that matters) which I'm then connecting to my ps3. (which has been converted to FAT32).

Any help fixing this problem is much appreciated.

[Baldrick]

I guess you have doubled checked so the subs are in sync on your computer first?

Another method would be to create an avchd m2ts using multiavchd.