I've tried adding a script to be started in /etc/rc.local which looks like this:
sleep 30
cd /home/user/
AMDOverdriveCtrl -b -i 3 .AMDOverdriveCtrl/5770.ovdr >> logs/overdrive.log
AMDOverdriveCtrl -b -i 0 .AMDOverdriveCtrl/5870.ovdr >> logs/overdrive.log
But when I start up my mining rig and run aticonfig to see the clocks, they're the default ones, and cgminer reports that the GPUs are unstable.
Could it be that AMDOverdriveCtrl successfully sets the voltages, but then the clocks, for some reason are not set? the log file logs/overdrive.log shows that the script indeed has been run, but for some reason it either doesn't persist or some other program changes the clocks.
When I log in and run the above script manually, it sets the clocks and voltages fine, and aticonfig reports the clocks that I specified in my .ovdr files.
EDIT: Solved