Well, it's not only Aftermath. I tried Awakenings too and the same thing is happening. I've even tried without the campaign file, they're still not visible. I'm getting this error (from Awakenings, but virtually the same error comes up with Aftermath):
Error: Am2.fs(62):
Error: Required token = [$multi_text], found [$mirror: 0]
File:parse/parselo.cpp
Line: 551
[This filename points to the location of a file on the computer that built this executable]
Call stack:
---------------------------------------------
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[ This info is in the clipboard so you can paste it somewhere now ]
That error pops up about 12 times, with different lines. Look's like it's something in the FS2 mission coding. Also, Aftermath is complaining about not having IFFs. So I went in, looked, and all the ships lack their IFFs... I don't know what happened.