Can you watch on the service tool or a PI that the car steps correctly at the slowdown point for each floor? Remember the slowdowns are binary coded so the car knows which floor it's running into. So if you watch the FS leds in the controller say send it from bottom to top. First yo should see the FS1 flash, then you should see FS2 flash 3 times ( up slowdown, floor level, then down slowdown) then you should see FS1 & FS2 flash 3 times for the 3rd floor, then FS3 flashes at the slowdown and comes back on when the car stops at the 4th floor. And it only overshoots 2 and 3 in the up direction? Not 4? Maybe a problem with FS2 traveler or input, its common to 2nd and 3rd floor. If that all checks out I would say maybe bypass is in too far but it would overshoot & relevel at the top floor too.
