Reaper and Ableton don't seem to be able to work with mpeg 4 clips. What is the best way of converting or repacking these files for work?

My interface disconnects randomly, flashing and switching my sound card to on board for a couple of seconds before turning on itself again. It's apparent in anything, from video, playback or DAW recording. It never used to do this? And I should mention it's very random. Sometimes every minute...