As with most homes the builder only really did the code minimum, so they didn't tape ductwork. This isn't a cheap home either, just corners cut and our first home, so it's a learning experience. Most people in our development are in the same spot.
I agree on the temp increase, but then I was going to shut down vents in the different rooms that are hotter to try and even things out a bit.
Our thermostat (Trane z-wave) only has auto/on, so the honeywell may be a little better there.
One of the neighbors retrofitted their house with 4 zones for $10k (incl. system and fixing knock-down). We're not willing to spend that much. I looked at this...
http://www.thisoldhouse.com/toh/video/0,,20810706,00.html
Interesting approach, just not sure on longevity (sharp edges, duct screws, duct cleaning...etc). Also a friend of mine brought up the issue of having too much pressure if too many zones are shut down, burning out the motor.
We might end up insulating the attic better (r-46 now).
Really hoping the home energy audit with IR camera shows some damning evidence. Most HVAC guys in this area build for the big national builders (incl. ours) and don't want to start stuff with them lest they lose out on huge contracts.