Would you mind sharing the code with which you create the vApp and the internal vSwitch?
We deploy the vAPP using a template and the command:
New-CIVApp -OrgVdc $org -VAppTemplate $template -Name $vappname
The variables are read from a .csv file but there isn't anything special there.
Once I can verify exactly how our vcloud polls vshield and vcenter to do the networking and can sanitize some other things I will get them posted.