Nevermind, I think I figured it out.
The P5N-D has two auxiliary heat sinks besides the CPU sink, and one of them is located directly beneath my GPU (which was the only component that was showing a heating problem). I think that the built in temperature gauges were picking up ambient heat from that heat sink. Also, that smell that was coming from it might just be because it's a brand new motherboard, as it seems to be lessening with time.
Thanks for all the help though, I'll be sure to keep an eye on it just to be safe.