I'm not sure if I'm having a related problem or not, but I now (after updating to 10.6.6) cannot use the eSATA docking base I use for offloading files to bare HD's. The drive will sometimes be recognized but more often not when I'm attached using the SATA cable. If I use the USB cable (this is a dual interface dock), the drive will be recognized for a couple minutes and then self-eject the drive....weird.
Sorry if this is a threadcr*p but it seems slightly related to what's happening to you.
FCP 7.0.3, PPro CS5.5, MPro Octo 2.8, 16 gigs RAM, Matrox MXO2, Sony EX1