I use a treadmill whenever I am working offshore, no-one likes it if you try and run for an hour round the heli-deck, and you get very dizzy apparently.
What I have found is that after the first couple of times my hips hurt(?) and also the balls of my feet, like you I set it for 1% - 2% incline.
I also have done long sessions, good for the concentration or switching your brain off, was this session longer than you have done before? Were you varying the speed or going faster than normal? What part hurts anyway?