Lewis...think I can guess where your airbase problems are, but it will probably take some checking, and hand-editing. So...here goes...
I'm guessing one (or more) of your airbases are missing a needed entry.
The tools needed would be an xml editor, and excel.
For each airbase, especially 'new' ones, that do NOT use the stock files, or modified, they need their own ID entry in the global_layer.
That ID must also match with the airbase entry in the qclocations.xml. If the airbase is new, or modified, there's a good chance it will need it's qclocation entry edited, or added.
There is also a chance the airbase entry in the cutscenes.xml could be missing, or needs to be edited.
(If you chose an airbase, but it defaults to another, this is probably the culpit.)
Keep in mind that all the stock airbases 'share' several files. So, many of the entries in the qclocations, and cutscenes are also shared.
Hope this helps! (I also prefer to manually add my bases.)