Thank you very much for the reply Repetier, I did not enable auto leveling. I think it is time I moved to v1 actually.
after more testing I think I have found the issue:
These Specific TMC2209 drivers (FYSETC) came from factory with 0 ohm resistors across the UART enable/PDN pin, this had forced my drivers into UART mode and I believe this was causing some interference with microstepping/steps, as the UART/PDN Pin was connected to MS3 (as soldered by factory) and im not sure RADDS is a true ground on those switches, but I have removed the resistors and I have not had issue yet.
Lesson learned hopefully, should have fully inspected the drivers before installing.