What type of subtitles are we talking about? (Also can you read the file in e.g. Notepad?)
Possibly the subtitle-file itself is not correct. Often downloaded subtitle files not only need a time-shift but also need to be "stretched" or "shrinked". For text-based subtitle files I always use
Vladimir's subsync which is a very simple and basic utility, which does the job it is supposed to do perfectly for only three types of subtitlefiles, i.e. SAMI, SubRib and MicroDVD or .smi, .srt and .sub. Other subtitle utilities are (i.a.)
SubtitleWorkshop (which covers a huge number of subtitle-types and has a lot more options and possibilities) and
SubMax, but I've no real experience with those.