Permalinks broken after using wordpress importer

Hi,

I have used wordpress importer to import posts from an old site on the same server, I am keeping the new site in a different directory behind a 503 so that the duplicate content doesn’t effect rankings. The thing is after I did the import (all the posts are now there) all the permalinks (navigation) on the new site no longer work, in fact they take me to a “can’t find what you looking for” page. Could anyone enlighten me as to why this would happen?

Cheers,
Olly