This application hasn't been responsible for displaying a player since IPS 4.3 came out - that is when IPS added their own support for adding a player for uploaded and supported videos. Can't remember if I may have something in there that adds support for video extensions that IPS doesn't support natively - but the ones they (IPS) support are:
'mp4', '3gp', 'mov', 'ogg', 'ogv', 'mpg', 'mpeg', 'flv', 'webm', 'wmv', 'avi', 'm4v'
I will take a look for you to see IF my application is doing something that it shouldn't be doing - provide me with a link to a post etc on your site which contains an uploaded MOV or FLV file, please (if it isn't guest viewable, then send me somelogin credentials via PM)