Thanks for making things clear.

I have done:
sudo sh -c "echo 1 > 
/sys/devices/system/cpu/cpu0/cpufreq/ondemand/ignore_nice_load"
and can confirm that the boinc processes are run at full frequency on my 
amd64x2 (2.2Ghz)

-- 
ignore_nice_load ignored in processor scaling
https://bugs.launchpad.net/bugs/368809
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