Sorry for digging up this old thread but I have the exact same problem as Kristoffer.
I am running 1 episerver 4.62(demo licence) on server 2003 (all others sites are turned off in the IIS) and I am playing around with it in VS2005 trying to learn how it works and things are working good.
Then all of a sudden when am running the site to test an update, I get the error "License violation! License is already in use at another online site: http://localhost/EPiServerSample/ [_LM_w3svc..."
Wierd thing is I shouldent have anything at /EPiServerSample/ since I put it all directly under localhost.
I tryed the "License-violation-after-removing-a-second-site", it dident work.
I restarted the 2003 server and it started working again, however I have a feeling it will be back, because I think this happend to me before. So if anyone have a clue why this might be happening and a more permnanet solution for it, please post here.