Hm... I know something, and that is that when you change processor speed settings, they are saved in the files /private/var/db/SystemConfiguration/com.apple.PowerManagement.xml
and /Library/Preferences/.GlobalPreferences.plist
I don't know which is the governing, but I'd guess the former is. Note also that for the settings to take effect, the proper deamon has to be noticed (or simply restarted?) - configd.