Hey Guys,
Having a very similar problem to the OP myself. I just purchased a ThermalTake BlacX hard drive dock with USB 2.0 and eSATA connections. I've connected the enclosure to my Intel onboard SATA controllers #4 and #5. I've installed a Samsung SpinPoint F4 2TB hard drive in the dock. This is an EcoGreen drive, so 5400RPM.
When I first turn on my Windows 7 64-bit machine everything is fine. If I then hit the power button on the Thermaltake dock, the drive spins up, Windows detects it and I have my G drive. The drive works fine and when I am finished, I can click on Safely eject the hard drive and I can power down the dock.
The problem is the next time that I turn on the enclosure...the drive indeed spins up and the lights come on...but Windows doesn't detect it. I have to go into Disk Management and Rescan disks and it reappears.
I've tried connecting this to my Gigabyte SATA ports as well as the Intel SATA ports and the behavior is the same.
I found the KB977178 about Stop Errors in Server 2008 and Windows 7 due to drives which spin up slow. I am running that hotfix, but it hasn't resolved this issue.
Any ideas?
Oh yeah: the behavior is the same if I use USB 2.0 or eSATA.
Edit: The fastest way I have found to run rescan disks is to make a shortcut on my desktop which points to diskmgmt.msc. Then, action rescan disks.