I doubt this is an issue with having or not having the Mod, but I would still check and be sure it had the Mod before putting in 4 x 120 GB drives.
Okay, since it sounds like the drives do not have any needed data on them, do this,
Step 1. Go to debug and do;
co de format 10000 /reinit
co de format 10008 /reinit
co de format 10010 /reinit
co de format 10018 /reinit
This will put the partition starting positions in the proper place for OS v3 and ensure they are all in the same place.
Step 2. Perform a FULL FACTORY DEFAULT (4 LED flash) hard reset using the procedure found in the WIKI here;
http://wiki.procooling.com/index.php/Snap_Server_Resets
Now I am talking about a HARD RESET not a reset you do from the web interface. Just follow the procedure for a 4 LED flash (pressing the button 4 times). Do Step 3 right after doing the Hard Reset.
Step 3. Flash the OS again
using SNAP Assist. Do not use a different OS version (at least at this point). Do not use an old version of SNAP Assist (like used with OS v2), so make sure it is a version at least as new as the OS you are using. And note, I underlined using SNAP assist, do not do this from the web interface.
Step 4. (optional) Just in case that particular part of the OS was corrupt (I doubt it, but), repeat Step 1.
I bet this cures your problem. If not, there may be a more serious issue going on.
If that is the case, I have to ask, are you sure it was working properly before the OS update?
Okay, go do that, then come back and let me know what a genious I am (or idiot if it didn't work).