I make all my PCB’s on CNC mill. I’ll wait to see your files but, then will provides some tips that may help.
I generate the Gcode using CopperCam - you can download/try for free. The free trial is good for small boards (won’t reach the limit on small boards).
I would try Coppercam first as problem may be Makercam. I didn’t find anything that ran well on my Mac so, I use Virtualbox to run Window (and CopperCam). Example below…