Well, this is my theory, since I just replaced my shifter 2 weeks ago and it happened to me.

I replaced the stock -> skunk2 and the shifter got sizzling hot... There are small rubber bushings that attach between the shifter and the linkage, and because the bolt underneath didn't fit just right, i didn't use the bushings, i used the old metal washers (heat conductors, oops) ... and I didn't think anything of it... after I felt the heat that it was radiating, i put the bushings back on, and even tho the shifter feels an ink softer, the temp went down

JackO