I understand fluctuations in WU and reject rate when starting out a fresh run of cgminer, but what Im talking about is fluctuations in hashrate appearing after running for 24 hrs. For example on a fresh run my 7950s get stable as a rock 640khs, but when I check them at the end of the day they are fluctuating between 590-635 constantly, I also thought I may be because of coin/difficulty changes, but the fluctuations continue even during a specific coin. One strange thing is that one of the cards doesn't seem to fluctuate at all and stays at 640, btw the rig Im talking about has 6 - 7950's in it, running Windows 7 headless. And all this fluctuation immediately stops when I restart cgminer.
Well I do mine on middlecoin, and it wasn't an issue before when mining straight litecoin, and by "better" I mean more stable and higher hashrates when I restart cgminer. My cards also run average about 65C in temperature. Any ways if nobody know thats fine. If I offend anyone by asking my question here I apologize.
I know I am taking a risk of getting flamed for asking anything in this thread... but at least I though I would try.

Pretty sure you didn't get flamed, but "CGMiner runs better" is so open-ended that the question needed clarification.
Statistical variance means that anytime your restart CGMiner, or zero the stats, you'll get wild fluctuations in hash rate, W/U, reject rate etc until things settle down over a period of hours. The diff being set to 1024 right now only makes the variance worse even though eventually you should end up with about the same numbers.
I just zeroed CGM on a couple of rigs that are mining elsewhere. Both are 4MH/s rigs. One shows a W/U of close to 5MH/s while the other is under 3MH/s. Once they've been running for a day or two, they'll end up back at the same rate and with broadly similar W/U and reject rate.
In other words it's luck of the draw and restarting CGM shouldn't make any difference to anything in the long run.