Running via ethernet on a 64bit machine its unlikely to be overheads as Mach3 will not be running the parallel driver to generate pulse the pulse generation is I believe carried out entirely by the CSMIO controller, apart from virus software or windows itself maybe starting housekeeping or attempting to enter power saving mode I cannot think of much that would likely affect it in that way. Turn of any virus software if running and disable power saving and screen savers not much more you can do PC wise. If it occurs after that you may have to look elsewhere for the problem, I haven't used the CSMIO although have one ordered so cannot really advise regarding the controller I would just double check earthing and maybe add EMI / RFI filter if not already fitted.