Cylinder test model (HighRes) that I used to debug the stuttering when printing the same file with Octoprint or from SD card.
Played with Baudrate settings etc. And the solution was a setting in prusa slicer.

I enabled “arc fitting” which replaces the G1 commands with G2/G3. (firmware must support it)
Setting can be found under Print Settings→Advanced→Slicing→Arc fitting" 

Octoprint:

SD card:

Octoprint and Arc fitting enabled: