[UKönig]

I had a problem similar to that once. I tried having two active captain campaigns going at the same time. When I quit and reloaded, on the SH3 title screen, it would load to about 50% and then crash, without fail, every. single. time.
I went fooling around in the SH3 folders, and manually removed the new captain that I had just created. Then I launched the game again. Things seemed to be normal after that. So your problem suggests to me that the game is looking for a particular file/path to load at that moment, and it can't find what it's looking for. Either that or it finds a conflict. Since it doesn't know which set of data to carry out, and can't make a decision intuitively based on available evidence to choose the correct file at the moment of conflict, it does nothing at all (shrugs its shoulders), and drops you back to the desk top. Other times I had gone back into the control panel settings and ran the install/uninstall option, and found a category called 'repair', so I gave that a hit, and again, it seemed to work.
Otherwise, you may have to remove the game and do a clean install. Only this time, load your selected mods one at a time to test them out. That way if you run into a conflict with the mods, you'll be able to identify and correct which one was giving you trouble much faster and with greater certainty.
I am by no means very skilled with computers any more, so, there will be others here who are more informed about the quirks of this game and what happens when you mod it. I hope you have a place to start from at least.