Ok .. I have been reading the solutions to this topic: like putting category / tag into the permalink interface (does not work for me) - trying after deactivating all plugins (does not work either) and before now restoring my db manually I came across this and wanted to know if someone please can specify please from where to remove the index.php: is the file itself meant, or is it the path of the perma?
Many people have reported permalinks not working after upgrading to 2.6. In all cases, these people have permalink structures that contain "index.php". This is a bug, detailed here: http://trac.wordpress.org/ticket/7306
1. If you're using Linux/Apache on your webserver, you don't really need the index.php anyway. Try removing it. The index.php thing was only meant for IIS servers, which don't support mod_rewrite.
2. If you need/want the index.php to be there, then on the Settings->Permalinks screen, add some values in for the category and tag bases. The words "category" and "tag" will do just fine. As long as they are not blank, this should work around the bug.
any advice appreciated