had the same problems as you ....my video would error at 100% upload... after speaking to my host who kindly spent half a day changing the server config to get this to work..

Basically the server doesnt allow exe files so he installed ffmpeg on the server.. then he changed the inc_header file to point to this $sFfmpegPath = $sGlobalPath . "app/ffmpeg";

then he uploaded a new file called ffmpeg to use for linux servers... also after updating the php.ini file as mentioned above...

That see more is as much as I can tell you as I have no clues about servers.. but hopefully that may help in some way...