I have had this happen twice... once because of an electrical surge, once because of automatic "Microsoft" updates (grumble, grumble).
I do a custom campaign, and I notice it "copies" some file over, saving the duplicate whenever you go into this entry. I then start a campaign. The machine reboots, for whatever reason... I then restart DMUC, choose custom campaign... and reading in any of my saved games starts a crash. By the way, if I try to start a new campaign at this point, it lets me, but it is no longer a DMUC custom campaign, and I can only choose one of the original factions to play.
It appears that DMUC doesn't know the machine has rebooted, and tries to copy in what it thinks are the custom files but are actually the ones it copied over. The only way I have found to resolve the problem is to reinstall DMUC, but I am sure there are other ways.
Anybody else encountered this? And if so, how do I address it?