Hi Robin,
Nothing should have changed in the way that the Check Number Audit List report works in version 6.8B as compared to prior versions. The first place I would recommend looking is the Group Security, to see if the Adagio group you belong to has had this menu choice disabled by accident. If you have access to the Groups menu under File, edit the Groups and make sure that where appropriate the correct options are selected. If you don't have access, perhaps the person with Admin rights in Adagio can look at this for you.
New menu choices have been added to version 6.8B of Adagio Payables (such as Import batches and Purge Vendor Notes). I wonder if a checkbox was inadvertantly disabled when these files were updated.
I would also suggest opening Sample data for AP, just to make sure the report file itself is OK - I wouldn't expect there to be a problem here.