Oh I'm guessing you are bitten on the ass by SATA power disable mode issue...
I just realized you were telling us all along that this only happens after a soft reboot. I had misread that and though this was only happening when you booted one of the OS images. Damn, could have gotten here a lot quicker.
And I'm going to assume that your drive is connected to the internal SATA II controller (which I think you also said, but it was not perfectly clear).
If so then this is likely the problem:
http://forums.macnn.com/showthread.php?t=527384
You can do the tape trick, (or more brutally, cut the drive's connector pin traces) but another options if you have a PCIe slot free may be to get a SATA III PCIe card and run cabling from that to your drive, that will help with performance, especially of any SSDs you also connect to that controller. This is not hard to do for 2.5" SSD including mounting them outside the standard bays, and may not be easy for a 3.5" disk that needs to go in a bay, but check around online for options.