Hi,
Could you share some more details about this issue? I am mostly interested in the following:
1. What's the version of Windows HPC Server you are using?
2. How is your application retrieving job templates list?
3. What is the exact setup of permissions on your templates?
Normally when user doesn't have permission to submit jobs with specified template he will still see it on the list and will get an error on job submission attempt. The behavior you have descibed seems to be invalid, but I couldn't reproduce it so far.
Thanks,
Łukasz