I had the XML export problem with Suite 2.01, but the export XML file just didn’t open in AE, crashed AE in fact. It didn’t make Media100 disappear, and seems to work fine in the latest beta. I had that same disappearing act several versions ago when trying to export to QuickTime. Never figured out what actually caused it, but what seemed to stop Media100 disappearing in that case was logging out and logging back in as administrator and running Media100. You might try that, even though it sounds like voodoo, it might help.
More likely is Floh’s troubleshooting scenario. M100’s tec h support can help you.
Good luck,