This is just a stab in the dark, but since I think Media 100 runs on QuickTime, it must have a .hal component. Therefore, theoretically, you might be able to use Quicktime to convert them. Open on in QT, then go to 'export' and see if you can export a QT .mov.
If you find an answer please please post. I have a bunch of exported quicktimes myself from Media 100 that I can't get to play on my final cut system. Audio plays fine. Video is all white
I've done some research and while there's a downloadable transcoder from Media100's website, there isn't anything available for intel macs (My files played fine on my old Job's G5-with media 100 transcoder). But if you figure something out, please post.