It seems that when the vehicle is warm, the shifting problem doesn't surface as much. That's ironic for me to say, since I live in Southern California and couldn't imagine what the tranny would feel like while driving around Minneapolis, but it's my belief that the syncro design on the newer transmissions allows for a sometimes-rough gear engagement, in second and sometimes third gear - regardless of transmission fluid. This is not unlike the intermittent issues Acura and Honda owners have experienced on the CL-S, RSX-S and Accord V6 Coupe with their triple-coned syncros on the 6-speeds.
Friction modifiers, synthetic fluid, regular, durablend, whatever. One would think that these were all tested with the transmission before it hit the production line. The fact that Toyota and Lexus don't offer synthetic fluid leads me to believe that they feel there's no inherent gain in using it. These intermittent shifting issues happen with almost every single manual transmission on the market - the majority have no problems, the minority do. It's impossible to tell since transmission health is predominately dependant on the operator's driving habits, not just the maintenence. I do know, however, that the press cars I've driven have had the absolute snot beaten out of them, and they all seem to shift fine, all the time. I baby my car and have problems with second. Who knows.
The question you have to ask yourself is: Can you live with it? Most likely every owner of every manual transmission vehicle has had, at one point or another, some issue with shifting, be it into reverse, or missed third and went into fifth, or something. If the problem doesn't affect your safety or sanity, I'd just deal with it since Lexus build quality is constantly at the top of almost everyone's list.