I had the missing apps and reboots issues while on ThundeROM. The missing apps seemed to be the ones I moved to the SD card with Ti Backup. Although I never had a unmount issue with my SD card before installing the new rom and never saw an unmount message while using ThundeROM, I kind of attributed the missing app issue to some SD card issue because the missing apps always seemed to be ones I had moved the the SD card. I believe one of the ROM developers made a comment about apps2sd.
I went back to stock and did the VC update. I rooted my phone. I have not had any of these issues since. Although I have moved some apps to the SD card, I have been a little more selective about the apps that I have moved to the card. Anything that may have to do with a widget or run in the background, I have left on my phone.
I'll probably try another rom in a couple of weeks.or so. Hopefully the VC update fixed the SD card issue.