P3D v3 weird autogen suppression problem

I added autogen suppression tweaks to some scasm ground/surface/markings polygons which work for the most part other than randomly on some sessions I get to see some areas lacking autogen again. If I change time or anything to reload scenery the autogen comes back and stays their or if I restart the sim. My guess is p3d doesn't load the ground polygons in the same order every time, failing the tweak.
Any suggestions to prevent this?

Update: Not completely fixed it but I have been able to minimize the issue little further by changing from few large exclusion rectangles to several small ones in the afcad file.

Update 2: It seems xml placed custom library objects with noautogensuppression flag and scasm library objects/polygons with/without no autogen suppression tweak do not go well together, causing suppression anomalies in other/adjacent areas.
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