We have more than one Zortrax m200 printer and also changeable perforated top layers. And seems that this problem is actual for all of them.
Firstly, not always printer can success with autocalibration even if you are perfect with your fingers.
Secondly, I have found that when you screw this perforated top layer, it loses its plain... and even if autocalibration is succeeded, material for raft won't flow equally deep for all sides if detail is big enough as a result of not equal level for all bed. And this is not about bad calibration with 3 spring-screws under the bed, but about a little bit cranked perforated plate because of small screws or strained metal plate below (singly this plastic perforated top layer of bed is flat enough as I measured). Seems that calibration calculations cannot eliminate these imperfections of top surface geometry.
For this reason raft is not deep enough in all places if you print lager detail and it's warping.
Hope for solutions in the future or comments if this is not common situation.
I have this issue too with several perboards I bought bundled with filament.
This perf boards contact areas are silver and they all tend to lift in the middle.
Since using them I have to bend them as shown on the perboard maintenance doc and then can relevel with good results (0.1 -0.2 from center to the edges).
But that is only good for a few prints. Then the center lifts again and the difference is about 0.5-0.7.
You should check using spirit level tool if heatbeds are not crooked or something. Same to perforated plates and platform itself.
Well, platform seems to be flat as the heating bed.
I think, that this could be because of temperature changes - then top perforated layer begins to deform as its material wants to expand and as all corners and edges are fixed with screws, then center can only go up.
This can explain why center is always with the best fit and cannot warp, but the farther from center we go, the possibility of warping is rising.
When fastening the perf plate to the table, hold the center of the plate down while you fasten the screws.
You can also try pre-stress the perf board so that the center is slightly lower than the rest of the board; when you fasten to table, the center of the board will be preloaded against the table or at least reduced (It is recommend to do this with v1 plates, I've partially done it to two of my machines with v2 plat (partially because I was worried about breaking the boards http://support.zortrax.com/straightening-perforated-plate/).
One thing that i noticed is that some raft part accumulated under the perforate plate tend it to bump (with V2 perf plate).
After dismounted and cleaned it with acetone, I screw the perf plate on the header bed loosely, let it heating into the M200 then I tighten from the center to the corner.