Multi-Segment support requires Allow policies only.
With IB policies, if one segment (Segment A) can communicate with 3 segments (A, B and C) but B and C are not allowed, the users segment A will only be only able to communicate with their own segment (A) by default. This is because users in Segment A can act as a conduit of information between 2 blocked segments. So, the Segments stamped for all users in Segment A will be A only.
With Multi-Segment if a user is a member of Segments A, B and C, their Sites will be stamped with no segments and set to OwnerModerated Mode. This will allow collaboration between incompatible segments moderated by the site owner.
I'm not sure if you are facing these issues, but I don't think these points are currently documented.