How fast is your machine. My mill did the exact thing. Jogged just fine, but when I stuck in code it went all wonky at 45khz. I turned down to 35khz and ran perfect. I then changed the PC to a 2.4ghz p4 with 512m ram with a Lava dual PCI port card and it runs perfect at 45khz. My mill (Full size knee mill bit bigger than a Bridgeport) Now does full rapids at 180ipm X and 150 Y and runs the roadrunner file pretty darned fast. Before the new computer/card the fastest rapids I could get were 120 ipm each axis.
My feeling is it is a computer problem, not interference.