RepRap/Sprinter is fine for Slic3R PE and Duet - I use it all the time. The problem is the M900 and M907 commands because they aren't supported in RepRap firmware. My best guess is that it's because you've enabled wipe tower and/or ooze prevention and that's where the M900 and M907 commands are coming from. I'd say it's likely that Mr Prusa has decided to use those commands in his specific version of firmware. The other thing that might cause issues is if you have ticked any of the boxes in "Output Options" - leave them all unticked".
HTH
