I dont know if anyone else has had this issue, but on my rig I have 2 hdd. One runs XP and the other runs 7. Whenever I'm on XP and restart the computer and leave it alone it will boot into 7, but when it does 7 fail to boot and try to recover. Does anyone else have this issue?
It's normal for it to default to the newest OS as the boot OS if you don't make a selection. Are you staying there to watch it boot into W7, and does it show some kind of Repair Console error?
Sometimes certain apps will install and function fine, but W7 has issues with them, esp if they're not WHQL certified. I had that problem with ATI Tool. The app would install and work, but W7 kept having random issues booting up because of it.
You could also check Event Viewer for any apps that are getting system warnings.