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With all the various powersaving/heat saving technologies such as Speedstep and Turbo mode that Intel had in place not all the cores run at the same speed at any given time, even under stress. Only one of the cores at any given time will be showing the turbo speed and that turbo speed is rotated among the various cores. What you describe sounds normal to me. If all the cores slow down dramatically at the same time then you have thermal throttling. Still, you should not be stress testing this system any more if you are hitting temps of 100c.
As I said above, you need to demonstrate to the system builder that the system is running abnormally hot at stock voltages and frequencies if you expect to make a case.
What version of Prime95 are you using?