Hi Mate !
I´ve tested WAC 4.1 in this correct MOD Order:
01_WarAceCampaign 4.1_final_FULL_XP
02_WAC4.1 16k Atmosphere
03_WAC4.1 Realistic Hull Damage
04_WAC4.1 Fix
05_WAC4.1 no mines
06_WAC4.1 SubPen_animated_18.02.2010
07_Aces' Super Pens v4 WAC Version
No other MODs installed, only this above !
Look here, another Screenshot:

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Please look at the UZO, the textur of the DF-Antenna and the open Hatch on Deck are not corrected !!!
When I disable your MOD (my MOD # 07 from the above List) all the things are correct, no Problems !
Tested in Naval Academy !
Best regards,
Magic
EDIT: Tested now with LSH (in Naval Academy) and all works fine, no problems with the boat !!!