Did you do this upgrade form the marketplace? Does your server allow Symbolic links? Sounds like the link failed to create, but that still should not result in no router.php (we check for that specific condition).
delete those entries, then run an integrity check. If you see them come back, the it indicates there's a problem with one of the module's verify_db event listener - it's probably encountering an error, so check your activity log and debug log for any entries.
Yeah looks like I am responding to you in 2 places. You want to make sure that you've enabled Smileys in your quotas in Core -> Quota Config -> Active Text Formatters.