Have you tried to clone the VM using normal vCenter cloning (and have it apply the customization specification)? Does that behave the same way?
Regarding the BIOS settings...
The .nvram file stores the BIOS settings. By default, the VSC does not clone the nvram file.
If you want the nvram file to be cloned (so that the clone VMs have the same BIOS settings as the template), then you can have it do so. Here's how:
Inside the VSC install directory (which is probably C:\Program Files\NetApp\Virtual Storage Console\etc\kamino), you'll find a file called preferences.xml
If you edit this file with wordpad, you'll find the following on line 12:
<entry key="default.create.copyNvramFile" value="false"/>
If you change this to:
<entry key="default.create.copyNvramFile" value="True"/>
The VSC should then clone the nvram file in all cloning tasks.
I'm not totally sure, but I think you might need to restart the "NetApp vSphere Plugin Framework" service for the change to take affect.
Cheers,
Luke.