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.

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

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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.

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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.

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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....

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