2 ideas about this:
– When installing the hardware, did you adjust the PCI-Express lanes as suggested? I did not know about this when setting up our system, and we had some strange problems. Setting the lanes correctly did fix it.
– Get in contact with Media 100 support. I heard rumors that they are working on a small update to fix some things, and maybe you can get a beta copy to see if your problem is fixed. If not it definitely should get into the next update.
Btw., is a crash report generated when the application disappears? If yes, do you send them to M100 via the BugReporter that opens? Include your email-address in these reports, and I would guess that somebody will contact you.