Thanks for the reply, AnalogKid!
Right now, I have a bunch of caps off the board as I've been testing them, and I had to order a new soldering iron (a Hakko FX-888D to replace my $20 Radio Shack piece of junk!), so I can't test anything at the moment, but I'll check when I get them back on. I am pretty new to this stuff!
The 1.3VB and 3.3VB circuits on the mainboard are converted on the mainboard using MP1583DN chips from 12V coming from the power supply. That 12V is measured as specified. I never thought to measure the 1.3V and 3.3V while running. I only measured the power coming from the power supply. Once I get it together, I'll check those.
Looking at the schematic, on the 1.3VB line, there are a handful of electrolytic caps in parallel and a bunch of little SMD ceramics. That 1.3VB supplies part of the main chip on the board. It also goes to part of the tuner riser. I am not sure where it goes or what it does inside there.
Here are all the places on the schematic that I can see where this 1.3VB shows up:
MPS buck converter:
Here is the datasheet to that converter:
http://www.mouser.com/ds/2/277/MP1583_r3.1-371539.pdf
Feed to big heat-sinked processor:
Feed to RF tuner: