When i re-installed my steam version i had trouble getting it to work, seemed that i had to make sure every single folder related to the game was deleted.. also that JGSME mod utility had to go.
Re-installing the game and uboat expansion at the same time messed it up also!
Had do do them one at a time, then reinstall the JGSME if your going to add a mod...and test without first.
Seems you are losing alot of quality time on this..but you have gone so far so keep at it
You`ll forever wonder what the problem is till it`s fixed.