It's a very long time since I had anything to do with CFS2 & I've forgotten most of what I knew about it.
From the information you've given I assume you haven't modified airbases.dat. Please double-check that the runway numbers run in sequence & with no duplicate entries. The same applies to the ID numbers although from checking a replacement airbases.dat included with the Fox Four campaigns it's normal for the gaps in the default numbers that you mention. This starts happening after the [runway.5] entry. ID numbers 9000 to 9077 are the old CFS1 Europe airfields (prefixed with an asterisk *) & 8000 to 8052 are the CFS2 defaults. You appear to be missing 8052 which is Iwo Jima.
[runway.125]
id=8052
name=Iwo Jima
base_lat=N24 47.02
base_lon=E141 19.01
base_alt=180
heading=236
allegiance=0
units_across=2
takeoff_start_pos=-500,0
takeoff_stop_pos=1600,200
landing_start_pos=5000,350
landing_touchdown_pos=500,0
landing_stop_pos=-250,0
The easiest way to check this would be to replace your airbases.dat with the one included with the Fox Four campaigns. This contains all the original default entries with the Korean bases used in the campaigns added. You will find it in KWCFS2_C4.zip posted here -->
http://simviation.com/lair/cfs2koreaRS.htmExtract the file to a Temp folder & look in the INFO folder. You can back up your original file before replacing it.
Please let me know if this helps.
PS. I assume the airfields that do show up in the Mission Builder are the CFS2 defaults. It's quite possible that the old CFS1 airfields won't be listed as the ETO scenery is not included with CFS2.