In my experience of using VLC it can be a bit slow to start playing. It may even jump over the first few secs as it opens the file & may also miss the last few. Some programs understand incomplete files better than others.

I guess I have the luxury of having xtra codecs such as mpeg2 playback for QT & also as a Pro user. But are you aware you can downld xtra plug-ins for QT playback for free. Go to QT Preferences>Plug-ins & press the MIME settings button. Now select the plug-ins. Also go to Update>Install New 3rd party QT Softw. After installing go back to MIME settings & enable them. Also, go & get these plug-ins:
DivX http://www.divxmovies.com/codec/
XviD (see link on above divx page.)
3ivx Delta http://www.3ivx.com/ (choose download) If you don't already have it.
And DivX Doctor II (link on same page as 3ivx download page)

I have QT as the default for certain types & VLC as default for others such as the windows formats. Just a suggestion.