I had a problem that manifested itself as a hot rear rotor last year.
When I first got my bike, I drained the brake and clutch fluids and replaced the brake pads. I just
mashed the brake pistons in, even though it was kind of hard. What I should have done was
rebuild the calipers instead of mashing those dirty pistons in to put on the new pads. So -
is it easy to mash your pistons in by hand? The difference between mashing in contaminated
pistons and clean happy pistons is large.
After I got the real problem fixed, I was further confused by my still too-hot rotor. When I rebuilt
the caliper I cleaned and redid everything, new rubber booties, fresh caliper grease on the
pins that the caliper slides on, everything - except I didn't clean off the pin that the pads
slide on. The fat new pads were trying to slide on the dirty part of the pin:

After I cleaned that pin, no more hot rotor. And fantastic brakes, both action and feel.
-Mike