I had a similar issue with my printer. In my case the problem arose when printing higher than a few centimeters. It seems like Marlin FW has some problems with round/sqrt to much After switching from GT2-20 timing pulley to GT2-16 timing pulley those problem vanished.
I always have an older Repetier FW ready in case such problems occur to verify if the problem due to FW issues.
I always have an older Repetier FW ready in case such problems occur to verify if the problem due to FW issues.