So I did a little more testing before work. I powered up the game, started a new game. Saved ASAP. Dumped the save data from my Duo to the bank, uploaded another saved data. Checked the BIOS memory manager. Put the Tennokoe Bank back in, and then copied the data back and it worked.
This leaves me with a few possibilities, one is that only certain conditions exist in which the save file data gets corrupted, the second of which might be some problem with the other Duo and the Tennokoe Bank.