Then would you say that pool stats like what BTC Guild provides you with would be more accurate then their CGMiner?
Yes, if it's a large enough time period.
Days. So it seems to me that only 1/3 of my Jupis are up the advertised speed of 550

530-550
480-500
230-300 (Runs really hot at 300 so hot that the case is almost uncomfortable to touch.)
Indeed that's a perfect example of why the default binary was substandard in that regard. If you have that much heat as a problem, check they didn't mistakenly leave a bit of plastic between the device and the cooler... that's happened to someone on this thread.