I think I am inclined to agree with your assesment. In my previous post, I mentioned I ran fix permissions in the disk utility, and my problem (which was consistently happening within a few minutes after rebooting), disappeared for nearly a day, then came back sporadically for the next 24 hours (2-3 times), then today I was back where I started, with no more than a few minutes after booting before the big freeze. I came back to this thread to post my failure and saw LordBBK's post. I did think my Mac Mini (3 months old) was running pretty warm, but dismissed the thermal failure theory because the symptoms did not seem to fit. I mean I was getting constant failures, I run disk utility, reboot and they go away - immediately! I did not turn off the power and let it cool for any amount of time!
Regardless, since we all know that hardware failures can be much more elusive than software bugs, I thought I would give his suggestion a try. I rebooted in safe mode and installed the fan control program. I figured that since safe mode disables some of the more advanced graphics functionality, maybe I could get the controller installed before the box froze again. It probably took me more than 20-30 minutes to do, as I didn't realize that Safari wouldn't work in safe mode (it just clocked), so I ftp'd the package from my other Mac that I had downloaded the package to.
My initial fan speed - I think was 1800 RPM. I bumped it to 2300 & rebooted into normal mode. It's been up 4 hours now.... I not ready to say we've found the root cause here, because I've been here before, but I post an update tomorrow and let you know how it goes! Fortunately, I still have 9 months of warrenty left!
Many thanks to LordBBK & Mr Pi ! I am beginning to feel hopeful !!