I think you answered your own questions there. Move the missions you're trying to select to mediavps_3612/data/missions.
The reason I said that this was probably a UI or file structure issue was to assure you that you didn't need to worry about your FSO version number or any software bugs.
e: it's also possible I'm completely off about what's causing the issue, mind; until I'm actually sitting at an FSO install looking at FRED I can't really give you good advice. But try it!
But...the missions have ALWAYS been in freespace2/data/missions.
They were there when the CM was working fine, and nothing changed.
If the CM was only able to see them from within the MVPs folder structure then Fred2_Open as whole would not have been able to see them - but it is, I can work on the missions fine from the retail folder, just not see them in the CM.
Moved as suggested, no luck.
Resetting.
BH
ps. Bu thank you for the suggestions