Check if USB legacy is disabled in BIOS on this PC.
There is a chance that you have unique installs of EEPC on each hard drive. You should check the admin console to see if you have a duplicate object of your machine name. Export the keys for both the original object and the duplicate object. Then use those keys to decrypt each drive individually (using WinTech). It will probably be easiest to only have one drive inserted at a time. Be sure to use the Workspace Functions in WinTech to validate that you are using the right key for each hard disk. If you don't know how to do this, call support and get to tier 2.
By the way, you can prevent this from happening in v5.2.1 and later by using a defscm.ini file on the server before you build your install set. There is a new option that will treat the drive in the multibay properly. The exact name escapes me, but I know it is possible.