A year or so ago I had that problem for no obvious reason. I think I fixed it by starting the game and waiting until it got to the main menu, then clicking on the Resync Mods button at the bottom of the screen. It will take a minute or two to finish, so be patient.
If that doesn't work, exit the game and go into your Documents\My Games\GC3Crusade directory. Rename the folder Designs to DesignsOFF and the folder ShipStyleSet to ShipStyleSetOFF. Start the game and try Resync Mods again.
One of those worked for me. If neither works for you, I'm out of ideas.
Thanks, OldSpider, but that didn't work for me.
When I check the debug.err file, there are lots of "FAILED" lines regarding Civs I've never subscribed to. Very strange, indeed.
The only thing I can think of doing is to uninstall the game, make sure that the whole directory is empty, then re-install it.
I am looking for a clean slate here.
Does that sound like a plan?