Problem with GWX/SH3 Commander
 

I've been having a problem with these two mods for Silent Hunter 3. Whenever I begin a patrol, I have to do it through SH3 Commander. After that, I always have to run it through the GWX Silent Hunter 3 application. If I try to change anything at all in my career, or even if I try to run the game from SH3 Commander, I always get a CTD and it corrupts the save file. Is this normal? Am I only supposed to run the game from SH3 Commander the first time and then just run it through the GWX application from there on?

No, it's not normal. You should be able to run the game either way, but using Commander every time is best. If it's crashing then something is definitely wrong.

I'm not sure what, though.

Do not make mod changes while not in base between patrols. That is one of the causes of CTD/corrupted saves.

And always, ALWAYS, roll back SH3 Commander when you exit SH3. Either manually or with auto-rollback.

If you try to change anything in your mod setup without rolling back SH3 Cmdr, you will corrupt your game and a reinstall will probably be necessary to get it working again.

Don't know if you are running a super mod or not, but if you are running GWX, you need an additional file for SH3 Commander for it to work properly.

Not sure if that is the problem or not though based on the information given.