It is worth noting what the Hauptwerk CPU meter is trying to show (rather than making inaccurate remarks) (manual pg 130):
CPU - The meter indicates the approximate estimated peak audio CPU load/stress. Red indicates audio CPU overload or audio driver synchronisation issues and likely audio glitches (try reducing the polyphony limit, increase the audio buffer size, or check for updated audio drivers). More specifically, the meter shows the amount of time that Hauptwerk is taking to calculate each chunk of audio as a fraction of the amount of time the audio driver has allowed Hauptwerk to do it. Note: the meter doesn't show the same thing as the operating system's overall CPU usage figures. Hauptwerk's CPU meter is specifically designed to show the risk of audio glitches, which is heavily dependent on audio driver performance and the performance of other computer hardware/driver components, as well as overall loads on the computer's CPU(s).
Doug, provided the meter doesn't go red whilst playing your should not hear any glitches. It may be that on startup there are some issues... do you hear any "noises" other than perhaps the organ wind coming on at startup? Apparently some "sound modules" can take a little longer to set their parameters which may be what's going on.
Iain