In simplify 3d, i try to use a skirt on every print other wise my extruder can't get enough out right away. However in only Simplify 3d, my delta printer stutters about every mm. This only happens on the skirt. I have tried repetier and it does not do this as simplify does. Suggestions>
What's your "first layer height" set at? It could be that when your skirt is printing, it's a little too high and isn't making immediate contact with your printing platform. If your first layer height has a lower percentage, it could be adjusting for this height issue, so you don't see this problem on your first layer.
If I'm right, try lowering your Z position (overall height, not tower) .05mm at a time, see what happens. But if you hear scratching, quit the job fast!