Turning off one processor with CHUD tools

So I need to turn off one processor on my MBP running leopard 10.5.4 to solve a sound problem with Myst III Exile. When I switch to just one processor in the processor preference pane the computer slows down, which is normal, but what doesn't seem normal is that there are processing spikes that happen every 5 seconds or so. The computer seems to freeze during these spikes. I'm not running anything out of the ordinary. I have my linotype font explorer running, transmission torrent client running and thats it. Once I turn the second processor on again the computer functions normally with no spikes. Any help would be appreciated.

Thanks for stating the obvious, does anyone have any intelligent suggestions rather than casual observations?

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