Try this!
Enable this mod in JSGME
Start GWX (without SH3 Commander! Make sure it's rolled back!)
Fire up a single Mission! "Brake" or any other. Chose sub VIIC (not the VIIC/41) and a date that that is between 43 and 45 to test the different Towers!
If the sub works in Single Mission then it works!
IF you want to try this sub in Career. Start the game via the GWX (no SH3 commander)
Pick name; and flottilla that has VIIC's. Pick the VIIc (not the VIIC/41 )
Chose a year between 43-45.
And try it!
If one of those doesn'T work, then there must be conflict that eludes me!

Of cause I take it you installed ti Sub correctly!