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The joys of having an old machine *shrug*
The app is using YOUR processor, so it claims cycles. So, how fast is your procesor, how much RAM do you have, etc. With a couple of gigs of RAM and a 1.4 Mhz Athlon XP processor, I never saw a freeze with the toolbar app trying to map proteins or whatever it was doing, but some of the folks running a 633 Celeron with 128 megs of RAM did notice a few glitches.
I am inclined to think something else is the cause of the troubles you experienced.
I am running Google Compute on my Duron 800MHz with 512MB RAM and MS W2K, without a problem. The latency of my computer's reactions is a few milliseconds higher, but not annoying enough to stop contributing to an excellent cause :-)
What operating system is your computer running?