The problem is that I stoopid.
I had the ammeter after the ignition switch instead of BEFORE as I had assumed. Since the alternator was connected to that, it charged the system, as it was supposed to.
I thought I had it the other way around and everything else I had done assumed that. When I put a diode on the only wire that was after the ignition switch, and the thing ran on, then I knew I was stoopid.
Oh well. At least I figured it out. I was rewiring the thing while working from home on various support issues and obviously got confused.
I stoopid. But at least I figured it out and fixed it. It works as designed now.
DOH!
