Joey,
Maybe we should just let this be, now that you've satisfied yourself.
But I'm not quite sure I buy the 'gear slop' theory. As long as you are tuning up, the string is going to continue pulling back on one face of the gears, and I don't see any way the gears are going to sort of settle in to a middle position.
An experiment might be in order. Alternate, every other string, tuning up or down. I'd go three down, since you have more experience the other way. Check your tuning again at the end of playing, and then the next day.
My guess is you'll find the ones you tuned up are already somewhat sharp by the end of a lengthy playing session, and the ones tuned down a bit flat.
The reason I asked about nut slots is that, especially when tuning up, any friction at all is going to leave you with the portion between the nut and tuner with a little more tension than is on the rest of the string. I don't care how perfectly fitted and smooth your slots are, I'm convinced this is going to happen to some extent.
The vibrations of playing for a while would help this to equalize (sharp of your original tuning), and maybe there would be some slight creep while sitting quietly for a day (though I think this would be much less).
I also tune up, but have a regular routine where after turning the key, I press on the string between nut and tuner, probably over-equalizing it slightly, and then pull on the string (slightly harder than I would usually play) back around the pickups.
Of course, I could be wrong, or at the very least a bit obsessive...
-Bob