Agustin,
Did you reinstall first? It won't fix what you describe but the dotlrn installation was broken because of site_nodes.
Anyway, I've noticed this behavior too. I was about to post about it after doing more tests.
On my side, I get a "file not found" when I go to the admin pages, but I don't need to restart aolserver, just to reload the page (I'm using firefox 2 on debian). It happens also on openacs when applications are added, so I guess there are still issues with caching.
Malte, any ideas?