I always close my CAM/CAD software (and Winamp) when cutting stuff, and leave the computer alone until the work is finished. Actually, considering the fact that that's about the only software I have on my CNC computer, I'm more afraid latency-wise about auto-saves and auto-update attempts than from actual resource drain. Disabling the screensaver, energy saving features on Windows and the BIOS, and anything that might pup-up unexpectedly (like auto updates) is a must, too. Keeping the machine offline helps a lot. No antivirus, of course, which is another reason to have CAD-CAM on the same computer so you can keep the cnc computer *almost* isolated from any potential risks (there's always the need for ocasional resources that sometimes you can't get offline like reference images and stuff like that).
About a year ago I tried Mach in my software populated, antivirus running, "non-cnc, everyday's use" computer (online and other stuff) and it worked perfectly (I even had a couple of accidental screensavers popping up and the machine just kept going!). This computer "passed the test", got a clean install and became my CNC machine.
About a month ago I tried one of my machines with my newer non-cnc home machine, which is a lot faster and has more and faster RAM, and I lost a lot of pulses. I guess you never know which process might be messing with latencies, since a lot happens on the background without someone noticing (even more when online). I've noticed that some motherboards (and/or CPU's, can't be sure) might be more likely to latency problems (perhaps because of some built-in BIOS features).