By default when a vAPP is created it creates a new port group within the associated vDS.
From testing and learning the hard way it seems the first uplink listed in the vDS is always assigned as the active uplink in the port group for the vAPP and load balancing set to “Route based on the originating virtual port ID”.
This of course means you cannot setup teaming/EtherChannel on the physical uplink ports and whichever uplink is assigned needs to have the same VLAN ID as is configured for the vCDNI.
Debugging the problem:
In my situation the vCloud environment started with a single host and direct attached storage so only had a single vDS which had the port groups assigned for management, vmotion, external networks and to which vCDNI was associated too.
This caused the situation that our management uplink was always selected as active uplink for vApp port groups create, since it was the first listed uplink in vDS. We however did not want to assign the same VLAN and have traffic flow over the physical management ports, physical separation always best in my opinion.
Created a separate vDS on which I migrated the management and vmotion port groups (virtual adapters) too, as well as another for my external networks. This can be accomplished without downtime when you have 2 or more uplinks associate to the vmkernel
On the vDS which is associated to the vCDNI I removed all the uplinks.
(On each of the uplinks, the associated vmnic has to be removed first before you can delete the uplinks from vDS, this is accomplished by the following:
Select the host
Select configuration tab
Select vSphere Distributed Switch
Select Manage physical adapters.
Click remove for vmnic from the uplink name.
I setup two uplinks on the vCD associated to vCDNI and assigned the same VLAN ID on both of the uplinks physical ports.