Matt,
I've waited for some others to make some posts; now... I wanted chime in, once more, with my (refreshed) opinion(s)... Again, these are just my thoughts [grain of salt, eh?]...
First, let's consider that you actually have TWO problems here. What are they? Well, one is clearly the firmware on your Barracudas. The other, well, that's a bit more gray, or more correctly (in this case), pink.
Step 1) Separate the two problems.
Step 2) If your data is important to you, back up your data... IMHO, while separated from the DNS-323. Pull the drives and direct-link one directly to a PC. Back up your data and then flash the drive. Set it aside.
Step 3) Search this site for "pink". You'll find a few posts that may give you an idea of what your dealing with here. My suggestion? Reset the device to factory defaults. (Do it all. Do it all the way. That is to say, "graceful shutdown and hard restart"... E.g., shutdown cmd, pwr off, unplug n/w cable, unplug pwr, then wait for the electrons to die off.) Reverse the process. Flash the firmware to whatever ver. you want. Repeat the graceful shutdown/hard restart to verify your flash took.
Step 4) Install the freshly flashed HDD into Slot 1 (the one on the right), prep it up (part and format, etc.) -- DO NOT SET UP A RAID!!! If everything looks okay to you, COPY (not move) the data you backed-up (to the PC) before to the Barracuda through the LAN. Then, wait and watch... hours/days/whatever.
Step 5) When you're satisfied, i.e., no pinkage after working data back and forth... flash the other Barracuda (on a PC) and, in this case, I would wipe it, too. Install it in the left slot on the DNS-323, prep it up, and set up a nightly sync or copy routine, or whatever you want.
Again, I'm pretty new here and I am not an expert on this.... Just thinking out loud. Good luck.