Have also this problem.
After the 2 update process I made so far, all my disabled scenery were enabled again (double gate position back on world map).
The solution was to remove all disable entry, then update and finally disable again. As I have more than 10 disabled airport, this is tedious ! Is there another solution to reactivate the disable list, or better a way to solve this problem ?
EDIT:
In fact, just re-adding one disabled entry, trigger the "apply" button, which, in turn, allow to reactivate the whole disable list.