Two different USB 3 HDD docks - disk partitioned on one not usable on the other
The problem will lie with the dock disk-controllers and the method they use when translating the hard disk layout. I recently serviced an HP NX7400 laptop and the BIOS has two different modes for dealing hard disk translation - LBA Assist and Bit-shift. 

Both work, but if a drive is formatted using one method it will not be recognised if the other option is then selected after partitioning and formatting.

The acid test would be to format both disks, one on each dock, and then hook the drives up directly to a Mac. I suspect one of the drives will be recognised and accessible but the other will pop a "Disk Unreadable" message and prompt to be initialized.