Did you ever find a resolution to this?  We are experiencing the exact same issue between our UCS and VNX 5400 in both of our data centers.  We are on ESXi 5.5 U2.  We have the issue when using a VM Fex VDS, a VMware VDS, or a VMware vSwitch.  We have a mixture of issues as not every host has the exact same issue.  Most of the hosts do not show all of the Port Groups being used, but some show all of them used, but the number of Connected Targets do not correlate that.