I've got the same issue except I have finished the game, all the missions are locked apart from the last 2. I can press X to view stats on the completed missions. gutted. was looking forward t ghosting the missison I got spotted in, but I don't want to play the whole thing through again really.
Looks for me like it's because I tidied up all the autosaves, I thought it would use a single save file to save progress, and not a different one for each mission - http://support.gamesas.com/?i=4444&l=en
But even all the knowing doesn't help you in a battle against a Bethesda game.
I played the jail escape mission and then (of course) the sewer escape. In the main menu under missions the first mission was selectable. After completing the sewer escape and entering the next level, the first mission in the missions menu became grey and inaccessible. This is rather strange because I did not delete any autosave. I thought leaving the autosaves untouched would let you select and play finished missions through the missions menu or did I get something wrong?