I was coming to this board to report this exact problem it seems.
We're playing local co-op a and had a few problems along the way. Two players had their saves corupted in a crash and one of us had his save rolled back loosing a few levels and his more recent weapons. This resulted in players falling behind and currently haven't finished WL1.
When we finished WL2 with me as the player1/host (never had any problems with my save) the ark ship and new difficulties did not unlock. I tried then to finish it solo and it worked. Happy times! The others joined again and we played the very first mission on the new difficlty setting (expert?) and afterwards that difficulty got locked again and the mother ship popped up again as the new unlocked mission as if I never beat it.
On that first mission we played though it remembers us finishing it on expert so we could continue on that one mission on hte next difficulty and so on. Now we have finished that one mission on all difficulty settings but can't access the higher settings on any other mission and we can't play the arkship. We are currently stuck with nothing to do basically and no way to progress but with a huge desire to play this game so we need help.