Didn't stumble across ar solution to my problem here (sorry, if it IS already posted, though). Had trouble with the PermaLink feature and archives (by month) not working. Found the solution myself: under "Options->PermaLink" in the field "Use the template tags above to create a virtual site structure:" enter only slashes and variables (index.php etc. is OK though). Do not enter any other characters as this will mess up your archive pages (throws 404 error). The reason for this is the buggy construction of the .htaccess file. A fix maybe?
Post a reply, if I was helpful. To feed my ego. ;)