Well you have to remember that Hyperthreading makes the system appear to be a multi-processor machine even though it isn't. Essentially its the hardware simulating a multiprocessor environment w/o one actually being around. This will make multiple applications running on the same PC appear to run faster then when only windows is controlling the slicing. In games though, and other high end applications like PhotoShop, it actually slows the applications down as its taking from their usual time slice and doesn't allow them to override the default running window. So yes they will slow down.

In short, as others have said, the only fix is for your players to turn off Hyperthreading.