Oops. Should have mentioned that I've done that. Apologies. I just turned on the machine last night, and it happened again, so I was in mild panic mode when I asked the question, and left off that important detail.
But my partner, who works on Macs all day long, every day in, day out, did that for me. We swapped out one of my other internal hard drives, booted from it, etc. And after the "fix" it still happens. And I try to remember to repair permissions every few weeks.
So far, it eventually launches and everything is fine once it's up. And most of the time I just put it to sleep instead of shutting all the way down. But it is a little disconcerting when it doesn't start up first time. And this behavior never happened to me on any past Mac operating system...maybe a few times before system 10.0, so this is a totally new behavior after I moved to 10.6.6
I'm leaning toward moving to 10.6.7 to see if this fixes it. Of course, after backing up. I'll let you know and Rounik know how it goes. Thanks again for the support.