Ok, I just ran a bunch of tests. Because I'll need to explain what I found to the furnace people as well, I put it all in chart form. (Plus, my job has me analyzing stuff all the time, so this is a bit normal for me to do.)
http://img163.imageshack.us/img163/290/furnance.png
To measure gas flow rates, I went outside and watched my meter. The quarter foot needle spun fast, so I watched it spin and timed it for 1 minute. On my power bill, it gives a direct ratio for BTU per cubit feet. Here in Utah, we have high quality natural gas, so it's 909 BTU per ft^3.
For what I saw, the downstairs furnace appears to be stuck in the first stage. But it is definitely consuming natural gas at a decent rate. The upstairs furnace seemed to go a bit beyond what it says it should burn in BTUs for stage two.
I'll have to try forcing the downstairs furnace to run on high fire. But I'll need the furnace people to work with me on that (I can't void any warranties.) Overall though, it seems that I'm losing a lot of heat into the slab.
The upstairs furnace heated quickly. So quickly, it didn't appear to radiate into the walls and furniture. I just had hot air.
I turned off the thermostat, and let the room stabilize back down to around 74. Comparing the BTUs used, it seems the downstairs furnace needed to use about twice as much gas as the upstairs furnace to heat a floor. Ugh.