We are having the same problem here. I am guessing that the admin course does not follow the same schema as every other course, but the "Upgrade Course" link on WeBWorK is somehow only using the standard course schema.
I am actually curious about how these tables are actually used in an admin course, since I'm not familiar with problem sets or such ever existing in the admin course.
Any feedback on what is causing the database upgrade to flag these issues? (If you delete the two extra fields, the admin course recreates them later.)