Turn off all CV options, both in General Config and the Settings page, and see what it does (With CV mode on). Generally, the only CV setting you need to use is "Stop CV on Angles".
But try to avoid exceeding 100% FRO.
I´ve discovered that if I speed up above a certain rate, much lower than the machine is capable of delivering, the distance travelled in both X and Y axis is not accurate ; (. But the machine does not loose steps nor position (due to the encoders) as I can G0 X0 Y0 Z0 and it goes back perfectly to the work piece zero point.
This certainly sounds like either an issue with your drives, or a mechanical issue.