The subtitles are all 'ripped' from different media, or from different versions of the video (theatrical release, directors cut, extended, unrated, etc). Some come from PAL, so are 25 FPS encoded, some from DVD (29.97), some from Blu-Ray (23.976). If you put a 29.97 subtitle into/with a 23.976 movie, they grow out of sync. I have not looked too closely at the contents of the .srt subtitles to see if this information is contained within the file, but I suspect it's not. Only one or 2 sources for subtitles show the FPS information at all, and even then, many of the options have no information about FPS.
I'm not sure there is any good way to 'automate' the correction of this during live playback.
I think the pluging being updated to do a better job of picking the 'right' one is your best bet to get this situation resolved.
I'm spent quite a bit of time looking for subtitles in Spanish for my current collection, and have experienced this frustration myself. It's a bit of a crap shoot finding the right subs currently.