Issue: Area Contents listed twice

Verify that you don't actually have 2 copies by going to the wiki admin panel > Integrity > URL Conflicts, and checking for any entries there. I don't have this problem myself.

Just checked there. Says no conflicts were detected.

In phpMyAdmin, verify that the table vw_route has a PRIMARY KEY on the column routeid.
If it does not, please attempt to create the primary key using routeid.

Yep, I checked there. Routeid is the Primary Key of vw_route.

Huh, so I just visited my wiki again and now the duplicates are gone. The only thing I did was adjust the friendly wiki urls (went from index.php?wiki/&title=Prefix:Article to /wiki/Prefix:Article). Though even if I switch back, the duplicates are still gone.

I guess this issue can be disregarded for now. Fingers crossed that it won't pop up again.

I removed the duplicates. It seems the upgrade script was not able to create a unique index on vw_counter.routeid
I am still trying to figure out why that might have happened.

It seems the 4.0.4 upgrade script still had vw_counter.pageid as primary index in memory at the time it was trying to create a unique index on vw_counter.routeid, even though vw_counter.pageid was already removed. Because its memory suggested a unique index already existed, the index on vw_counter.routeid was skipped.

This issue has been resolved for new 4.0.3- to 4.0.4+ upgrades by a new build of 4.0.6. Sites that have already been affected by this issue (even if they don't know it yet) will be fixed by the upgrade to 4.0.7 when it is released.