Maybe the bed is not completely flat? And since the autolevel might not be perfectly configured it might mess something. Do you have access to the original configuration.h file? You can increase the autolevel points and also adjust the probe position
My printers:
-Makerbot TOM (#5215, circa 2011), MK6 extruder, ABS 3 mm
-HICTOP Prusa i3 (modded for auto-level, thread screws), ABS/PLA 1.75 mm
About me:
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