Clean URL / URL alias bug

I have a multisite configured in addition with the Domain access module. Everything worked fine, until all Clean URLs which begin with 'node' stopped functioning. I guess this is not a mod_rewrite problem since the server configuration is the same what it was when it worked - and the Clean URL setting page gives a green light for it anyway.

Unfortunately there has been a lot of changes and I can't tell at which point this problem occurred. Menus work, l-functions work, and so does everything else I have tried... except for node/xxxx, node/xxxx/edit, node/add etc. The error they give is 404.

However, '?q='-URLs do work in these and all other cases too.

Any help is appreciated.