I know from personal experience
that if you have more than c.200 airbases in a single install, you'll run into trouble trying to get them to show up at all, whether FF, QC or MB.
The fact you can see them in FF & QC suggests that maybe you're near this limit (MB is a lot less tolerant than the game itself), or as MR suggests, something is amiss with the airbases.dat entries. Just adding the scenery will allow the bases to show in the FF & QC listings, but you need to add the airbases.dat entries to use them in Mission Builder.
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