What PowerShell/PowerCLI version are you running?
Does this work if you're connected with an Org Administrator account? Might need more permissions than a "vApp Author" has.
I tried on my vCD environment with PowerCLI 6.0 R1, I didn't run into the same problems, but I am logged on with a vCD admin account.
Get-Org TylerPG - this returns my Org
Get-Org TylerPG | Get-OrgVdc - This returns my Org VDC
Get-OrgVdc -Org TylerPG - Same as above
Get-CIvAPP -OrgVdc TylerPG - Returns my vApp
Get-civapp -Name vApp_system_1 -Org TylerPG - Returns the same as above (I only have one vApp at the moment).
I suspect its a permissions issue.