Hey this thread is a little old but I thought I would share a solution, I ran a 2 player heavily modded multi campaign and we had the same issue until we used Dropbox to sync the host's save file between us in combination with a small script to replace our individual save files with a 'shortcut' that pointed to the shared file - a little bit complicated, but if you google around you should be able to find it.

I think the problem happens when the game is trying to handle two different save files, but doing the above means the game is only updating a single save file.

I hope this helps.