Seeing this same issue:
when I deactivate ACF 5 Pro and reactivate ACF 4, and then go back to ACF 5 Pro, I get prompted to upgrade the database again, and each time I perform the upgrade I get another copy of the field groups.
Seems like ACF should be avoiding this duplication somehow or tracking whether the upgrade has already happened. (I’m on the edge of whether ACF should support upgrading, downgrading, making changes, and upgrading again.)
