Hello Trekdork,
unfortunately i cannot help you with your problem. But i know what you're speaking of since i have a similar problem with the ship designer (shipyard ingame). Several designs i have created don't appear in the game - even when all available techs in the are researched.
I don't know what's the reason for that strange behaviour. All i know is that it is not depedent on the hull size since the missing designs are from various hull sizes and from every hull size is at least one ship design there. Maybe someone else can bring a little light on this affair...
My version of ToA is 2.02.030
Best greetings
Midnightrunner
Edit: I found out that the problem affects only the ships - not the templates. On some missing ships the available room is maxed out when i try to upgrade them in the ship designer from the main menu, on some of them it isn't so that can't be the problem too. Ingame the templates of the missing ships are available in the shipyard so i think it's related to the installed components somehow...
Edit 2: I found the reason why my with the ship designer designed ships are not appearing in the game. It has to do with the terran-specific techtree and is related to techs you cannot research if you're playing the humans. I will list a few of them which i was able to sort out by going step by step through my designs, removing one sort of weapons, saving, quitting the game and restarting (maybe there are even more techs since you said that all of your ship designs are not there in the game). So here is what i found out which weapon techs are available in the ship designer, but shouldn't be there because of the tech tree for the terrans:
Disruptors / HD Spike Driver / Quantum Torpedo / Anti-Matter Torpedo / Subspace Blaster / Singularity Driver / Kinetic Stream
These weapon techs are available in the ship designer when you choose the terran style but don't appear on the technology tree and are therefore not available in the shipyard when you invoke it from inside the game.
To the developers a question: Which program for ship designing shows the correct techs for the humans? The Ship-Designer you can start from the Main-Menu or the shipyard you can start from inside the game?