Ah, okay -- loading this up in the latest beta 3.043 version (which will be official on Monday, with whatever last fixes), it's easy to see what the issue is. But I can see why you were confused. These ships are all stored in your fortresses on Mudic, where I guess you put them in order to keep them out of the way during a fight or something along those lines. In the version you are playing, ships inside transports are simply invisible to the Find interface. On the later versions, it shows them parenthetically so that you can still find them when they are in transports. At any rate, you've got a huge amount of stuff on Mudic, so that's where you can find everything you need for now.
