I guess I was one of the few.
I think I know what it is. After a mission in a campaign is finished you can save it just fine, quit, and come back to it later. However, if you save right after a mission is done, *then* select the next mission (and it's mission specifics show up) and save again (if you forget if you saved like I do sometimes) then it'll jack up your whole campaign. No 'fly' button then. I'm fairly sure that's what it is.
In other words, save before you click on the next mission coming up. If you save it while viewing details on the next mission and you save it, it will basically think that you've not finished the mission nor any of the prior ones if you come back to it at a later time.
Just an "Eyes Out".
Nef