I piddled around with it this morning and I am stumped as well. I wrote a few missions back last spring and I don't recall it being like this.
Everytime I set up a Gato for a mission, it gets assigned as a 'neutral' ship. When I place the Gato, it is on the Allied side, but when I look at the Gato's properties immediately afterwards, it says 'neutral.' :hmm:
Then I tried setting up a Balao mission (Balao is correctly listed as 'Allied'), and the Balao does not appear in the mission's ingame drop-down box for sub selection...the Gato is there as is every other sub type, but no Balao.
We desperately need tater or lurker to chime in with a little help!