Roger:
This is a result of the Intersection Priority strengths of the Building Materials used for the Roof and Wall. You can either make the Roof stronger than the Wall (when using the Connect command), or use Solid Element Operation (SEO) rather than Connect.
You should add a Signature to your Profile (click the Profile button near the top of this page) with your ArchiCAD version and operating system (see mine for an example) for more accurate help in this forum.
David