Wierd bug (SOLVED)

I'm experiencing an odd bug that I can't seem to find and smash. Whenever I run eternity fullscreen at any resolution above 320x240 I get these steady pauses in the game every couple of seconds. The whole game just stops for a second; rendering, sound, input everything. Doesn't happen at higher resolutions if they're windowed, only fullscreen. Doesn't happen in zdoom, but I have same problem with software mode quake. (several different ports) I've tried a couple of different monitors, graphics cards, even tried running from another hard-drive. My system is clean of viruses and I have no background processes hogging the cpu or ram. Eternity was running fine on this same box less than a month ago so I know this probably some kind of os glitch (registry etc) but I just cannot find the thing. I'm happy to wipe and re-install if I have to, but it bugs me when I can't find the cause of a problem first even if I can't fix it. So if anyone has any thoughts please share, I'm at a loss on this one.

Running XP pro sp2

Thanks,
Jack

EDIT:
I solved it. A system monitoring program I was running did an automatic update (this is why I normally disable those things) and the new display routine interferes with software mode programs every time time the meter redraws. Hence the once every second pauses, it's default redraw time. I found this after the re-install. (unfortunately) Everything was fine till I connected to the net. I was running a traffic monitoring program and it picked up the sysmeter trying to update.

Are the pauses in Eternity occuring at the same time as palette flashes due to injury or collection of items?

No they're steady, like on a tic. Roughly every 1.5 seconds, and the pauses are about half a second in length. Happens even in just a menu with no demo running when I'm doing nothing. Looks like it affects Eduke as well but again only in software mode, if I jump to 16bit or 32bit (which kicks in hardware mode) no problems. It's not the bit depth though because I can run software mode quake at 16 or 32 bit and still get the problem.

The effect occuring in diverse different games would suggest, then, that it's an issue on your system rather than with any particular game. But then I take it you were leaning in that direction already by your comments.

Correct. I knew it was in my OS somewhere, I was just hoping with the focus here being on a software only engine someone else might have had the same problem and could point me in a general direction. Well looks like one of those classic Windows reinstall fixes. I swear if it weren't for my love of about three games that won't function in linux....