Michel,

I've been avoiding to install SP 3 on our W2k systems (servers and professional) because it generates all kinds of weirds things. In all our W2K prof. systems it ruined IIS configuration at the point it never run again.
Now it seems in other case that when we started with a clean system with nothing on it except for the OS and upgrade it to SP3 and THEN, installed all the software it worked.
Not that I had a lot of time to investigate what happened but to me it was clear: I don't install SP3 on systems that I have everything configured, if I need to do so, I just start from scratch.
One of the systems, a W2k prof whose IIS went off after applying SP3 the only way we had to put it to work again was to upgrade to XP prof.

Good luck,