I got it working by disabling the NP port on either the uplink to the cisco or disabling the uplink to the brocade. The problem is that only one core switch (Cisco or Brocade different fabrics) can see the NPIV HBA's at a time not simultaneously.
I have the following scenario: IBM virtual bladecenter with build in Cisco MDS switch as NPV. This Cisco NPV switch is connected with NP port to Cisco MDS Director where I can see NPIV HBA's of different blades. The problem comes in where the  Cisco NPV switch is also connected to a Brocade Director where NPIV is enabled, but the brocade can only see the port PWWN and not the underlying NPIV HBA's. Please help if this make sense.
Brocade not seeing WWN's