Perhaps you could specifically list the gear that you have running things. Specific drivers, power supply, motors things like that. The configuration of your PC as well might help. It's hard to diagnose the problem with only the symptoms given and no look at the patient.
There are some on this forum who use EMC, but a lot of us use Mach3. Is there a possibility of you trying the demo version of Mach to see if the problems follow the hardware or the software?