Strange behavior from AVI ReComp

I've used AVI ReComp for a couple of months now to add subtitles on my DVD projects and I've never had any problems until today. I loaded the AVI file, which was my first "ripped" file that I was using to add subtitles to, using Magic DVD Ripper.

I loaded everything up including the subtitles and started the process, and also hit preview so I could watch my progress. The first time around the subtitles seemed out of sync, so I downloaded a subtitle from a different site.

That worked much better but then about two minutes into the process my video started slowing down noticeably and of course that through off my subtitle syncing so I aborted.

I'm thinking of just doing another rip of the DVD and trying the whole thing again. I might also look into loading the subtitles in Nero. I have Nero 9 but not sure if it does that. What other good subtitle programs would you recommend and should I just try re-installing AVI ReComp?