I have no experience with your particular printer, but I’ve had an issue where the bed was very sensitive due to being the edge of the adjustment range.

The bed screws on the Ultimaker 2 are manual screws with springs, and you can level the bed throughout most of the screw length. Having it at one end means the spring is quite loose, and things like weight and nozzle pressure affected the flatness of the bed.

So if you have an elastic tensioner for your bed, maybe set it at higher tension for a more robust flatness?

If you’re always adjusting in the same direction though, it’s not that, and is probably a software error where something doesn’t count Z-position right. Unless of course your printer is somehow getting longer?