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The docs suggest that certain registers shouldn't be messed with if the BUSY flag is set. I've tried disabling the General Purpose clocks, but the busy flag is always set.

See page 107 of the BCM2835 Peripherals document.

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I think you're finding a niche in our current user knowledge-base. – Jivings♦ Jul 19 '12 at 19:48
When I get an answer I'll record it here. – Dog Ears Jul 20 '12 at 13:06

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