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Following up.
I left File Shield unchecked all of yesterday and never experienced the CPU spikes.
This morning I turned it back on as an experiment and the spikes started again. I’ve had Web Shield enabled the entire time and have never seen CPU spikes with Web Shield enabled and File Shield disabled.
From what I can tell it’s definitely related to File Shield.
By the way, I’ve had Mail Shield disabled the entire time because I use Gmail via Sparrow, and don’t have a traditional POP3 setup.