Setting up materials for multi-building projects can be very tricky. There are several ways to go about it depending on the specific needs of the project. The simplest is to have a single master set copied into all buildings in the project, but it doesn't sound like this would work for you.
The trouble is that you have already started so it may be difficult (or at least tedious) to sort things out. The problem is that some elements (walls, roofs, floors, etc) call materials by name, but library parts store their references by ID numbers. I'm not sure about the profiles nor why they would be especially troublesome.
Do you have someone there who is experienced with Attribute Manager? I have some ideas about how to fix things up, but they are difficult to describe in detail.