The Madwifi drivers and Network Manager app seems to be causing a large number of wake ups. The worst is Madwifi which is keeping my CPU at C2 about 80% of the time. With wireless enabled I see the wifi0 interface as the top cause for wake ups almost always when I leave the system idle. The line in powertop looks like this: <interrupt> : yenta, wifi0
When I stop the Network Manager process and disable the wifi0 interface it goes to C3 state 90% of the time. When I enable Network Manager but keep the wireless disabled it's in C3 state about 80% of the time.
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