When I read the OP, I began to think it must be in the index shifter. Then bradtx alluded to it. I'm thinking that the shifter (when new) has to machined to precise tollerence so that the shifting is accurate. Like anything else with friction, over time...it has to wear down. And it probably is noticed first on the gears that are used...or shifted to...most often. So it might actually be a problem with the shifter.
Dan