Thanks for the help the issue was not having M564 H0 in my config file. Your "list of changes" page only describes this issue with Cartesian printers. Not delta's, so i was bit confused. I know you have a ton on your plate so again thanks for everything you do!
For anyone reading this, i have a delta with motors on the top of the printer. I had to change all my stepper motors too the opposite setting to get them to work again.
M569 P0 S1 ; Drive 0 (X) goes forwards
M569 P1 S1 ; Drive 1 (Y) goes forwards
M569 P2 S1 ; Drive 2 (Z) goes forwards
M569 P3 S0 ; Drive 3 (E0) goes forwards
Had to change is to
M569 P0 S0 ; Drive 0 (X) goes forwards
M569 P1 S0 ; Drive 1 (Y) goes forwards
M569 P2 S0 ; Drive 2 (Z) goes forwards
M569 P3 S1 ; Drive 3 (E0) goes forwards
and then add
M564 H0 at the end of my Config file in order to get my printer to home correctly. Also if you have code written for a probe that has to be deployed, but you are not using one on your printer. Remove it, it messes with the printers movement for some strange reason.