hmm ok first thing, when you have completed you 24 hr partrol and have sank waht you beleave to be a good haul and head back to your base, when your in the mouth of the bases port if you hit ESC on your keyboard, click exit partrol and then it should say in the bottom right hand corner 'Continue Mission' and Dock At: PORT NAME' you want to click the dock option. this will send you back to your home to do crew management and uboat upgrades, also you will receive a new grid to partrol for 24 hours.
As for SHC, you should always luach SHC first, then once you have configured the options, click the tick in the bottom right hand corner to luanch SH3, luanching sh3 then SHC may cuase problems such as your experiencing.
As for your mods, I suggest deactivate all you mods except for GWX, so your let with SH£ 1.4b with GWX mod only, then reactivate the mods that you want untill you see the file has been already altered box, if that does apear i strongly suggest you click no to adding the mod and dont activate that mod along side the others, as that is what will cuase you big problems to the point you will start to crash to desktop and have glitchs and bugs in game.
Heres a list of the mods i run with my SH3 with GWX that i no all work to gether with problems and make the game look and feel extra speacial:
GWX - 16km Atmosphere
GWX - Captain America's Officer Icons
GWX - Enhanced Damage Effects
GWX - Integrated Orders
GWX - Axis Mediterranean Aircraft Skins
GWX - Main movie - 'Das Boot'
GWX - VIIC41 Player Sub
No continuous 'Ship spotted' V1.2 for GWX3
Torpedo damage Final ver2.0
TorpedoTubesFfireFinal vGW
DBSM_SH3_Speech_Fix
Destroyers&Corvette
RadioMsg V 0.1
Real Depth Charge
Sobers 3D waves
sobers real smoke darker and a brown tint1.1
Ultimate Aircraft Soundmod
Von Hallys SOS Mesages
WB's Renown Replacement
Q Ship mod GWX3.0
BritishAsdicMkIFinal
Flotilla
LifeBoats&Debris_v4
GWX - Alternate Loadscreen - Full Circle
These are some of the best mods i no of and use, they can all be found in the SUBSIM downlaods, Silent hunter 3 section, use the search.
Hope this helps, also excuse my spelling and grammer it is 6am here!
Jonny