My battery tests at about 12.5V, but the ECU reading (using an OBDII scanner) as well as DVM reading at the fuse box read about 10.9-11V.

I believe this may be the cause of some of my other electrical issues, but I don't know why the ECU and fuse box readings are so low when the battery is nominal.

What could be causing this?

 

I assume this is with the engine off...
Make sure your terminal clamps and positive cable are clean and corrosion free.

Good luck, hope you get it sorted out..

 

Actually the ECU voltage does not increase even with the engine on (the battery voltage does, of course). It's as if something (?) is causing the voltage to drop, although absolutely everything that uses significant power (lights,HVAC, radio, etc) work just fine.

My thinking is that even with corrosion (which I don't see), I might get a reduction in current carrying capability, but not in voltage - yet something is causing the voltage to drop.