Hi Soeren, There is no special modification needed on the template. The RCU is simply calling a VMware supplied function via their API. A good place to start looking is the Virtual Center logs directory. On my lab machine, it is at the following path:
C:\Documents and Settings\All Users\Application Data\VMware\VMware VirtualCenter\Logs
If you sort the explorer window by date, and choose the newest vpxd-X.log file (where X is a number) you find the most recent log entries. Open this file and search for "sysprep" without quotes. The log should provide a reason for why the customization was not applied. The most common error we see in that the VMware Tools in the client is older than what is available. To fix this, you'll need to update the tools in the template or source VM prior to using the "Create NetApp Rapid Clones" wizard.
Keep in mind that the RCU 2.0 is a fully supported product. If you continue to have issues with the customization, you can contact NetApp Global Support for help.