For me it saves all wmos...So i have to find a situation how this appears.
Hmm please if you have this bug. Try to turn on F7 lines and see if you cant save WMOs if they are on 2 ADTs?Meens that they go across a green line. If thi is so tr to modify the adt beside that it is shown also marked as TO SAVE in the map menu (m key) and if it get saved then.