we also upgraded to 12 and had a similar problem couple weeks ago. Users couldnt see documents in access point that they were licenced to see. Permision sets on the files (qvw) themselves seem to cause it. These documents were listed as accessible to all domain users (Everyone) and local users (qvServerName\Users) but still no one coud see them. Even permisions by name didnt help. What did help was making a user group on the domain controler, assigning users to that group and setting permisions for the document to include this group (also disabling permision inheritance on the folder documents are in).
hope this helps.