Rooms will always sync with the last phase. Rooms in dRofus can only synchronize with Rooms or Spaces in Revit that are displayed in the currently active Phase. Room or Space Instances can only exist in a single phasePhase within Revit, and so it is not possible to have multiple Room or Space Instances across different Phases in Revit linked up with a single Room in dRofus.
If an item a Family Instance is created in a phase the room must exist in that phase or in a previously created phase in order to sync with dRofus items in rooms. If an item is created in a later phase, It will not show up in the room because it is not in the bounding box geometry of the room. The phase the item is created in has to match or exist before the room in which it was created inwithin a specific Phase in Revit, the Room or Space must also exist in that same Phase and that Phase must also be set to current in order to be able to view as well as validate the Family Instances in Revit against the Item Occurrences in dRofus for your selected Room(s) or Space(s) using the "Items in room", "Items in level/model" or "Items in level/model (spaces) windows.
The Phase within which a Family Instance is created has to either match or have existed before the Phase in which the Room was created.