I'm confused....we had several of our new students assemble our kit chassis this week, and I was watching over them quite a bit. I did notice that the bearings are thicker than the machined portion of the hex shaft, as shown in your photo. But we were very careful to assemble the transmissions as the instructions say, and they worked fine, no binding.
I know in the past we've had trouble with the gearboxes, when I was not so involved with the assembly (but did help with the diagnosis and reassembly), and we've had problems with gears installed backwards causing binding.
I really don't think that a thinner bearing is needed. But I also did not measure the shaft. Have you compared the dimensions of the questionable shaft, with those on the AM drawing?
http://files.andymark.com/AM-2566%20...haft%20Hex.PDF