I found this old thread about this, Locked. So I am putting up a new one.
viewtopic.php?f=57&t=18521&p=85474&hilit=locked#p85474
I have the same issue on a current game, once I load the save, all unlocked areas are relocked.
Unlocked Screenshot
Locked Screenshot
Custom map
Tiers.txt (4.09 KB)
Savegame
125 new.xml (2.63 MB)
Maybe it has something to do with the names of the areas? Not sure