I fixed this problem, but I would like to put some more info here as it is quite a scarce problem.
For the record: I am using a multi-store setup with some over 50 shops. Some blogs use template A, some blogs use template B. Only the blogs with template B have been affected by this problem.
The issue came from a fault while updating the rewrite_rule -rule in the database. (You can find it in your blogs’ table, example: wp_7_blogs) While you can’t edit this in WordPress as it is grayed out with ‘SERIALIZED DATA’. You can find it in your database.
After some searching in the database I found out that the affected blogs had a different value in this field. I replaced it with the line from the working blog and my damaged blogs worked again!
I found an older topic with the solution.
The guys in the link below made a script to ‘flush’ these rewrite_rules in the database, fixing the problem. Please read the full thread to see if you have the same issue and don’t forget to backup your database before using this script.
Read this topic for the solution
From the topic I can say that they ‘think’ the origin of this issue came from updating wordpress in combination with some plugins.. so I should have switched off the plug-ins before updating wordpress.
