Im using the latest SL3 internal build and trying to create a control template in blend 3 in the normal way. Unfortunately the "Edit template | Edit a copy" option is greyed out only 'create empty' is available.
I was not able to reproduce the issue. Please make sure you have downloaded the latest binaries (2009.2. 701). I am attaching a sample project that I created using the steps you mentioned. Have a look at it and if you encounter any problems, let us know.