Welcome Aboard Matey
To use GWX -
You must have SH3 + 1.4b patch.
The installation must be 'clean' (i.e no file changes or mods)
You can't use any previous career saves.
Other possible problems -
All mods (to be safe

) must be enabled whilst in port after a patrol.
Any file changes must be done the same way.
SH3Cmdr must be rolled back (if you use it).
Save Bugs, saving too near ports, ships or while submerged.
Possible solution -
Try loading the career save directly before you started having problems.
Try a new career to see if you experience the same problem.
Run the MD5 Checker program to make sure your d/l of GWX is not corrupted.
Last resort -
Roll back SH3Cmdr
Unistall SH3
Remove SH3 folder in My Docs
Remove Registry entries relating to SH3 (if you're happy doing this)
Reinstall SH3
Patch to 1.4b
Run GWX installer
Enable the Dec 23rd Fix's
Try again.