There is many theories going around. Air flow around the cylinders, or more oil is spraying up the rear cylinder and cooling it, or uneven intake distribution because of fluid inertia of the air and the way the intake strokes are set-up. I don't know. Maybe a combination of all, but the most sensible explanation is that the front cylinder does more work than the rear. 

The cause of this is due to the degrees at which the power stroke occurs for the front compared to the rear. Basically there is a longer lag time that the front needs to make up for.

The crankshaft does not spin at an even speed during the revolution and the longer lag time for the front cylinder makes the crankshaft slow just a bit more than for the rear, thus the front has to work harder when accelerating the crankshaft. The cylinder pressure is what is doing the work, and when the piston has a higher resistance to do the stroke, the slightly higher average cylinder pressure that is produced is making a larger heat transfer to the cylinder material.