More info:

I controlled the speedstepping by running BOINC  
(http://climateprediction.net).  After login or when I use
sudo /etc/init.d/powernowd start
the CPU goes up to highest speed as soon as the BOINC project starts running, 
and it stays there. Nice value of the process is 19.

When I stop and start powernowd like I wrote in my initial posting:
sudo powernowd -q -m 2 -l 40 -u 90 -s 100000
then the speedstepping is done in that mode and the CPU stays at low frequency 
when BOINC is running. The output is:

powernowd:   verbosity:Settings:
powernowd:   verbosity:        1
powernowd:   mode:             2     (PASSIVE)
powernowd:   step:           100 MHz (100000 kHz)
powernowd:   lowwater:        40 %
powernowd:   highwater:       90 %
powernowd:   poll interval: 1000 ms
powernowd: Found 1 scalable unit:  -- 1 'CPU' per scalable unit
powernowd:   cpu0: 800Mhz - 1866Mhz (12 steps)
powernowd:      step1 : 1866Mhz
powernowd:      step2 : 1766Mhz
powernowd:      step3 : 1666Mhz
powernowd:      step4 : 1566Mhz
powernowd:      step5 : 1466Mhz
powernowd:      step6 : 1366Mhz
powernowd:      step7 : 1266Mhz
powernowd:      step8 : 1166Mhz
powernowd:      step9 : 1066Mhz
powernowd:      step10 : 966Mhz
powernowd:      step11 : 866Mhz
powernowd:      step12 : 800Mhz

If I just do
sudo powernowd
passing no parameters to it, the output is just

powernowd: Found 1 scalable unit:  -- 1 'CPU' per scalable unit
powernowd:   cpu0: 800Mhz - 1866Mhz (5 steps)

which looks like the AGRESSIVE mode and not the one I saved in
/etc/default/powernowd. However, starting powernowd that way results in
the CPU staying at lowest frequency as well when BOINC is running.

So, there are two issues actually:
1.
Options set in /etc/default/powernowd arent used at all, no matter how 
powernowd is started
2.
There's a difference in speedstepping behaviour, depending on the way powernowd 
is started:
  sudo /etc/init.d/powernowd start => nice value ignored
  sudo powernowd => nice value respected

-- 
powernowd doesn't use /etc/default/powernowd anymore
https://launchpad.net/bugs/67341

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