If you have you’re using arcs, it is probably because it takes time to convert the arc commands to line commands in the mini rambo. If you’re not using arcs, then the reason is because the serial port (or sd card reader) isn’t keeping up with the movement of the machine. So if the planner runs out of little lines to execute, it will pause and wait for more.
There was a lot of tweaking of settings around version 425. The outcome was faster arcs. The settings were to adjust the number of lines computed in marlin to represent an arc. The result was much smoother, but only when you actually used arcs in the gcode.
I don’t think the planner is any larger in the skr, so if you have arcs off, I think the difference must be the speed of reading the commands. I don’t think just reading them over 250k serial would be any faster or slower. Is there anything else that is different? Are you using sd in one and serial with the other? Or maybe it is a poor quality usb cable?