Any differences are likely the MPlayer version. SMPlayer is a interface for MPlayer (which is user unfriendly by itself). Ports for Windows just don't seem to come out well most of the time. The last known good build I have tested from Sherpya is r33216, I have a ton of files I test with and had problems with builds after r33216, and better with r33883 so I decided to include that in the installer.
You can configure SMPlayer to use a different MPlayer executable. If you could test the same files with MPlayer2 from http://mplayer2.srsfckn.biz/mplayer2-20110831.7z
Extract it somewhere, go to the General prefs and change it to where you extracted it and change the MPlayer path to where mplayer2-20110831.exe is. It would help me out a lot, if MPlayer2 works better then I might consider using that. To reverse the change you put the mplayer path back as 'mplayer/mplayer.exe'
VLC WAS awful before 1.0. I watch a lot of fansubs, VLC did not support ASS/styling before 1.0 and it caused VLC to frequently crash, and showed "comments" which weren't supposed to be shown. If a line exceeded a certain amount of characters, subtitles did not show. Fansub groups exploited this to discourage use of VLC. In search of a player that did play a lot of formats and didn't install crap all over the OS, I found SMPlayer. Fansub groups always recommend a codec pack that puts crap everywhere.