It's a good idea to try to calculate the exact PPR from the belt ratio, ballscrew pitch etc. Trying to do it by trial and error shouldn't be necessary and you could end up including backlash etc. That's my view on it but there's probably no right or wrong.

Bizarre that MDI moves work OK but programmed ones don't, given that they both generate g code. You've got me there but one step at a time perhaps...