Similar problem here...
I have a Mac Pro, with 4 internal drives. Recently, I was using Adobe Lightroom, downloading some images through a CF card reader. Everything locked up on me. I attempted to eject the card reader, and the whole system froze up. After a few minutes, I finally shut it down by holding the power button down on the unit. When I booted it back up, one of my internal drives didn't mount, and I got the error message that the system didn't recognize it. It wasn't showing up in the Drive Utility either.
I opened the system up (after shutting it down again) and pulled the drive out, then reinserted it. When I booted up again, it was there, and working just fine. However, since then, it will just randomly unmount itself and give me an error message that it ejected incorrectly. Sometimes even pulling it out and reinserting it doesn't help.
Not sure what to do at this point, or if it's the drive or the connections or an OS issue or what.