Is that a Service Map? If it is, I think OBN is used and that won't work as indicated by SAP note 1620576:
The embedding of NWBC for HTML in the SAP NetWeaver Portal is not supported:
NWBC for HTML can be integrated in external portals in an embedded mode - that is, without a navigation frame - using the addition "/~canvas;window=embedded". If it is integrated in an SAP NetWeaver Portal, problems occur in particular with object-based navigation (OBN), for example, as it used in power worklists (POWL).
You should look into using NWBC for Desktop to access the portal, that way users will have unified UI.