I manually created an Area Group to place all components in the design into an Area Group using a wild card (i.e., INST "*" AREA_GROUP = "AG_MyAreaGroup" ;). Floorplanner recognized the Area Group and allowed me to modify it, but when I write the constraints back out, my new UCF does not contain the Area Group.
There are two issues related to this problem. First, you cannot use a wild card for all components in a design; your Area Group will not have any components placed in it. Second, only Area Groups with underlying logic will be created. Since the Area Group was imported without underlying logic, the Area Group is not written.