I have a deja vu. This was not working since many versions back. The same with Expense reporting. Once switched on, one could not switch it back.
You described one way of getting it undone: via the rebuild of the dimension, but that was too tricky in my situation. The chance of errors and data loss was too large.
In that time, I went into manual mode. Removed all Two-pass and Expense reporting. Added them again. Then excluded them from the dimension build. If a change was needed, I went there in the manual mode.
A quick check in the DBAG under Working with Rules Files, there is an entry explaining how to reset a property to it's default values. Under the Field Properties->Dimension Field Properties is a checkbox that reads "Delete when the field is empty" which should be selected.
Hope that helps you.
EDIT: Apologies for not reading your post fully. I'm intrigued now though.