"We’ll end with a recommendation: it’s sometimes better to overclock via the BIOS setup program. This is true both because of effectiveness (some programs don’t display the frequencies well, for example) and because of operating system choice (the majority of the programs we’ve mentioned are only for Windows)."
There are advantages to overclocking from windows too actually. Other than being lazy that is.
When you're booting your system at an overclocked state, chances are your vrm's can't keep up at powerup for some reason I don't know. So your oc will fail. That I assume is the reason that gigabyte boards shutdown and restart when changing such settings - to avoid the problem.
If you oc from windows, the changes being made are significantly less than from 0 to preset.
Regarding the programs - I have some comments on them. They might be brilliant in some situations, but they don't nessecarily work.
For instance on my work pc, a hp dc7800 with an e6750, setfsb can only read the fsb, it can't set it - no matter which of the 3 types I tried (mmt, slp and the other one). I suspect hp deliberately did something to prevent it from working. So on oem systems you may not find the solution you were looking for in software.
And atitool didn't work very well with my 8800gtx. It could set the gpu and mem speed, but the artefact check isn't able to figure out if the shader speed is too high. So even though it'd run 20 minutes scanning for artefacts in atitool, a 3dmark test would crash at the nature scene when the lights were rendered. So don't rely on the button to automaticly find the best frequency if the shader is linked to the gpu speed.
ps. on all ati hd48x0 cards I've seen so far, the max gpu setting available in overdrive (790 or so) seemed stable - no need to run the check