Frage S2-840 Uneven Z Axis

Hi,
Have just built my S2-840 and have been trying to profile cut 3mm MDF.
Some parts come out clean but others have almost 1mm uncut!
So I decided to check the Z axis depth to the HPL base.
I get around 0.9mm variation across the bed measured at 9 points. It doesn't ramp in one direction either, it is up and down.
Yes, I could mill a piece of MDF as a new base board but this will have the peaks and troughs so unless the material I am clamping to it is flexible I will still have the issues! The X/Y axis's seem to be spot on, I milled slotted corners of varying length and depth in separate passes working repeatedly around the corners and the slots lined up perfectly.
So my issue is only in the Z! I am wondering if my gantry extrusion is faulty, my parcel was damaged by UPS in transit but the only obvious issue was a bent baseplate.
Perhaps the gantry piece was damaged as well?
Does anyone have any suggestions on what I can do to correct / improve my situation?

I don't like the poor support the board has in the middle (only a screw).

I've been thinking in adding some wood chunks under the board to have a better support.

May be this can fix your problem.

Well slight progress, I fitted the TSlot bed in case the HPL was the cause. I would have fitted it to start with but UPS took 3 more days to deliver my second parcel!
I still have the deviations but they are a bit smaller, now only 0.64mm maximum, the trouble I have is though still that the Z is deeper in the middle and shallower on each side with X=0 being shallower than X=597. Then I also find that Y=0 is deeper than Y=837, though it at least appears to be linear.
It has been suggested to clamp and mill an extra bed sheet to take care of these deviations, this would be alright if the deviations were linear but having a dip in the middle will make clamping a nightmare and cause problems with stiffer material.

I tested mine and I get +-0.5 mm (1mm total) along the Y axis.

What I see is you can't depend on really exact Z jobs with this machine.