I haven't had any reboots on my D3 yet, but when I first got my OG Droid, I had a problem (about 1-3 days after I got it) where something caused it to get stuck in a reboot loop. It would go through full startup, be on the homescreen for a few minutes and then it would reboot. I took it to the VZW store (because I didn't know how to get to the recovery menu at the time) and he said there was some sort of activity queue that was probably corrupt and resetting the phone would fix it. So, he factory reset the phone, and all was well after that.
I don't know if this has any relation to your problem, but it is something you could try. If you've only had the phone for a few days, maybe it won't be so painful to get things reconfig-ed back to the way you like them since it is fresh on your mind. ;-)
-SR-