Hello. I can confirm the problem. Same thing happend to me after update 2.00 (or 1.98 i´m not sure). All steam missions was completed with use of BIS_fnc_endMission so they all have activeKeys active in user profile. They just don´t seem to apear as completed on mission selection screen. Notice that it applies only to steam subscribed missions. Oldman scenario and pretty sure all missions exported to missions from editor or mod would appear as it should. I´ve loaded the game without mods and DLCs.
In game it looks like this:
Also this issue might be duplicate of this- T155574