In case anyone is still watching this thread:
I have a BDR-206 in a nice Vantec external USB2 enclosure which was working perfectly in Snow Leopard that wasn't up-to-date. And I just updated my Mac Mini to Lion. Now the drive doesn't show up at all after boot. Nothing in the System Profiler or Toast.
I found out that I have to power cycle the drive to get it to show up. After that, it works perfectly again until I reboot. Then I have to power cycle it again.
I know this is hard for you people out there with Mac Pro towers, but you might want to try to power cycle the internal drive to see if it helps your problem. I know this isn't a fix, but at least you can see if works.
I'm still searching for more information or an answer to this.