So I created a shuttle, but for some reason, every time it spawns, the docking ports catch fire almost immediately, and then won't catch fire again later. I don't know why, I wired them in imitation of the Nibbler, but they just keep becoming the Mockingjay, even when it spawns as a respawn shuttle. I'm so confused, if anyone has any help, it would be greatly appreciated.

Depends how you connected the docking port. Docking ports take in power, the power output should be wired only to the batteries input.
When the docking port is connected to the rest of the shuttles power systems the power will try to go through the docking port, but since that power has nowhere to go it breaks it and sets it on fire.

Ill check again, but I believe I already fixed that