It seems that when you call msg_connect, the call to message_port_sub is not made until the flowgraph has been flattened, so the subscription does not belong to the hier block, it belongs to the block inside the hier block that has the message output. However, when you call msg_disconnect, it simply attempts to call message_port_unsub on on the hier block, which fails, as the hier block has no subscriptions." The fix simply checks if the source or destination blocks are hierarchical, and if they are, resolves which block in the hierarchical block has the message port, then calls message_port_unsub with that block.