I was wondering if your level up and level down sensors are symetrical from the door zones centerline, and set for a half inch of dead zone. Yes, I'm sure you thought of that, no doubt... But I have to ask it anyhow, because I don't exactly know what is meant by "dzu and dzd". Are those the two door zone sensors? Or leveling sensors? Anyway, if you run to the center floor, in both directions, can you adjust the leveling sensors to give a good stop? Is the cwt balanced correctly? Slow downs symetrical in the up and down? Motor field has enough oomph? (Volts) Howz it compare to the other cars? I've had cars that were adjusted wrong to compensate for other issues. Works until you disturb it.
Almost everytime I run into issues like this on older jobs, I find that the basics had been screwed with, over the years of late night quick-fixes, and goofy servicemen. When I get the basics corrected, everything falls into place. Even if this isn't the case with your situation, maybe something I've said will jog another thought with you, that will lead you to the answer. That's the way it is for me, when I bounce my thoughts off other people. fwiw
My two cents here. Encoder on gov. or car top? If on the gov. and it utilizes that spring looking coupling, it could very well be broken. One direction engages the broken section right away, whereas the opposite direction pulls the two mating faces away, so in effect, the coupling turns, but the actual encoder count is a bit behind. If this is a gov. mounted encoder, remove the encoder base fastening screws, and the tiny allen screws (careful, there could be two set screws in each hole) that hold the coupling to the gov. shaft, then gently tug on it...if it's broken, you'll know it. I have found after doing a floor table that both up and down floor levels are compensated for using the "Floor to High" (or Low) feature and I think they are adjustable up to 1/2 " max., and one direction does not affect the other. I have yet to get "dead nuts" on all floors on a basement installation...like you, some are within an 1/8 of an inch which is the best I can get. If a rail type mount, my bet would still be encoder.