Uploading marlin to printrboard, resulting in half speed/length etc

i just got this problem. never experienced anything like it and i'm having a hard time figuring it out.

So, i've run my printer for a long time without issues. suddenly i got some problems with my y axis skipping steps. in my troubleshooting i tested swapping the x and y motor pins.

this worked and the print finnished without errors.

so i changed the pins in marlin and uploaded the new firmware..
and i needed to change some directions and endstops in the code as well and uploaded a couple of times..


But now.. everything is correctly working, EXCEPT every move is half as fast and every move is half as long.
example:
i tell the printer to move 100mm +X at 40mm/s
the printer moves 50 +X at 20mm/s ( measured distance and aproximated speed )

and if i try to print something it will print it half as big and only utilize a 4th of the printbed.

Any thoughts?