Did you try the DataGroup Upgrade Utility on the file with no effect or just replace it?
The dataset is the same in Update 1 so no upgrades should be required. We changed the UI for the Floor Manager but as far as I am aware Floormaster.dgnlibs from the SS6 dataset should not need any action.
We have seen odd behaviours with Floormaster.dgnlibs brought forward from earlier versions, these do need upgrading as described in Upgrading Floor Master dgnlib from ABD SS5 to ABD SS6.