I am running vCenter 5.5.
I have had issues with deploying custom appliances through the web client because it does not seem to enforce the same rules as the windows client does. When deployed through the windows client guest customization is disabled, when deployed through the web client, guest customization is allowed, but end up wiping any vApp options that are included. These are the steps I've followed to reproduce this issue.
1) Deploy OVA
2) Convert vm to template
3) Deploy VM from template using web client
4) select clone options: "customize VM" and"power on"
5) do not change any of the hardware (just click next)
6) Input vApp options
7) Click finish
8) The VM gets created but not launched because required vApp options are missing (even though they had been filled in)
It is possible to then edit the vApp options again and fill in all the fields again and launch the server. Using the Windows client, this is not an issue because guest customization is disabled with the message, "Customization of the guest operating system 'otherLinux64Guest' is not supported in this configuration. Microsoft Vista (TM) and Linux guest with Logical Volume Manager are supported only for recent ESX host and VMware Tools versions. Refer to vCenter documentation for supported configurations."
Is this a known bug, or is there a way to prevent this from happening other than just knowing that guest customization shouldn't be used even if the client allows it?