There were a few bugs in the original build for 0.9.6 that caused problems trying to play .flv or .mp4 files that were using the H.264 Codec. When trying to launch from file association VLC would launch and do nothing. If VLC was already launched and you tried to play the files it would crash the player with a diffrent error message for both. If the logs were checked they would include statements that the system clock was going backwards.

If you download the latest version (it is still 0.9.6, just a newer build) It fixes these issues and many others that have cropped up since the new interface overhaul in 0.9.x. This is expected when ever you do a major overhaul of a program. If it isn't stable and polished enough for you go back to one of the last versions of 0.8.x untill the bugs are worked out.