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High CPU Usage on Alternating Cores

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I have been using XBMC Eden on Ubuntu 11.10 as an HTPC for some time now, and it's been totally stable and great (devs = rock). Then a few days ago got a notice that support for 11.10 was being dropped, so upgraded to the latest LTS version, 12.04. XBMC runs fine still, except for one small flaw...

Previously each of the four cores would run about 12-18% usage equally (with the processor stepped down from 3.1ghz to 800mhz) which would allow the cpu to run at a relatively cool 102deg (and a very nice 19db) Since the update though, XBMC will run one core at 100%, at the full 3.1ghz speed, and cycle between them every second or two, maxing out core 0, 1, 2, 3, 0...etc. This causes me to have to crank up the fan controller (which is doable to a degree) and the cpu run at more like 125deg. For obvious reasons, its much more preferrable for the system to run cool.

This pattern continues regardless of if theres a menu displayed, if theres a video playing, what the video format is, etc.
There is no tearing, no stuttering, no drop in framerate, the video and audio play perfectly still.
I have tried various fixes from Dr Google, including disabling the rss feed, making sure the dirty region rendering is on 3 (though setting it to 1 and 2 have no effect on the pattern), each of the vsync options available, and two sets of FGLRX drivers.

None of these have had any substantial effect, with the cores still running at 100% in cycle... any ideas why, or what to try next would be appreciated.

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