I've been doing it via perk select. Changing the XP required for Level 2 to 1 and adding the perk to blue's L2 perk list added the perk itself, and I verified it was working by adding a different system (a weapon system, if I recall). I'll build a test room next time.
However, it works now. And it definitely didn't last night. I tried adding different familiars, too, (since I assumed they might spawn atop one another and have the same leash, making it hard to see), and that never worked, either. Adding other systems (like a weapon) this way worked fine. At this point, I had been assuming that it didn't spawn the familiar automatically.
I've been relying on ctrl-F4 for XML reload, does that act any differently than an actual game restart?