I've had problems inserting pre-designed units in the alphax.txt as well. The biggest one is that they don't appear on the pre-design lists at all, ergo, the AI remains clueless about them. I'm pretty sure I've input all the parameters correctly, including special ability tags, to the letter. When I tried giving a custom faction of mine a free Fungicidal Former, I got some weird-looking 1-1-1 unit instead, with an icon that looked like a city on a black asteroid. When it fought a mindworm it promptly crashed the system.
I've tried designing a Probe Foil, Probe Cruiser, Needlejet Colony Pod, Police Citizens, and Clean Guards, but nothing showed.