I've read before that someone had this happen to them but can't remember were I saw it.
My home built CNC running on MachIII does not run the coded vectors smooth. It runs just fine then will pause for like a second or two then run but after a bit will pause again. Some times it will stop running the code two or three times in X or Y movement every three or four inches.  I don't know if the problem is in MachIII or my PC controls. Seems like I had read that the PC speed may be too slow. But this problem has just started about 3 or 4 mouths ago using the same PC.

Any thoughts?