Braveheart,
No, if I understand your problem correctly, I don't think that it's a scenery problem. It is probably the difference between the [ruway.XX] number in your airbase.dat file and the number used by the mission's author. It is not uncommon when flying any add on campaign.
In the airfield.dat file in the Info folder, each airfield had a couple of reference or index numbers. Example:
[runway.71] <<<-- This number must match up
id=8560 <<<-- No duplication in your airbase.dat file
name=FR - Bordeaux (Merignac)
base_lat=N44 54.37
base_lon=W0 27.44
base_alt=54
heading=90
allegiance=0
units_across=2
takeoff_start_pos=100,0
takeoff_stop_pos=1600,200
landing_start_pos=5000,350
landing_touchdown_pos=600,0
landing_stop_pos=-0,0
; NDB 324
Your runway number needs to match the number used by airbase.dat file of the author in the mission.mis file. If not, you get the problem you just outlined when using the "M" button. It must also be in proper ascending sequence in your airbase.dat file.
There have been several attempts to produce standardized airbase.dat files to prevent this, but with the plethora of bases worldwide by numerous authors, it has been dificult for everyone to sync up.
I think that Rami usually includes his airbase.dat file with his campaigns, but it may not sync up with the Aces High data used by DD.