How long of a ride does it take for the seal to start leaking ?
Does it leak statically without ever having ridden it ?
Does the surface of the shifter shaft look OK, no obvious damage, gouges, grooves, etc.?
How far in are you installing the seal ?
My last best place to go after this, is the negative battery lead where it is bolted to the transmission, the bolt is hollow, or should be hollow, it is the vent for the transmission, check it for obstructions.
A wild guess here is that when the transmission gets up to operating temperature, it is 'pressurized' due to the heat, and air can't escape, and the shifter shaft seal may be the 'weak link' in the system.