Looks like it's because of my experiments with removing the ship limit (partially successful, but the network code needs to be edited to make up for it.)
I think if you make a file called debug_filter.cfg you'll get some debugging info auto-saved...sounds like the problem is that for whatever reason, your campaign (cs2) file ends up having more than the max number of ships saved in it, or thinks there's that many ships.
If you can use a hex editor, check the value 16 bytes after the campaign name...if you can't can you post the .cs2 file up here for perusal?
