download vobsub and use the subresync tool in it to fix up all your sub problems. it can convert from microdvd(.sub) to subripper(.srt) and also .sub+.idx to .srt which is useful if you want to change frame rates as sub/idx is limited to the original movies framerate.
also subtitle workshop is a pretty good alternative as well
media players on the pc are very lenient when it comes to subtitles, renaming doesnt work, if the file format in the actual subtitle file is different. convertxtodvd is more stricter so try and use .srt where ever possible as its the most flexible. if you are doing pal->pal or ntsc->ntsc sub/idx are fine