The only time I've experienced one pipe hotter than the other, I had a blocked idle circuit and I thought the bike was idling on both cylinders, but it was only idling on a single cylinder. Once I accellerated past the idle circuit range, the other cylinder would begin to fire and I had normal power. That normal power had me assuming that both cylinders had to be firing all the time, but they weren't.
I could get the bike to idle at about 1100 rpms on one cylinder with no problem. The side that wasn't firing was popping and farting occasionally and I thought it was because of ignition issues (I thought the spark was cutting out. The air coming out of the exhaust seemed warm on both sides at idle so I also wrongly concluded that both cylinders were firing. If I spit on both header pipes, one would instantly boil off the spit, the other didn't smoke at all... That made me realize that I wasn't getting any firing on that cylinder until I was at about 2800 rpm. I realized that it was the idle circuit that was clogged, so I wasn't getting combustion on one cylinder at an idle. I unclogged the idle circuit, fired the bike up, and spit on both header pipes which both boiled off the spit instantly in a puff of smoke at idle.. fixed... If it's not hot enough to boil off your spit, it's not firing.