Steps to reproduce:
1. Create a template named "A"
2. Import it and create new project from it
3. Make slight change in the project (like composition title) and save as template with same name.
4. Import updated template.
Now you have only 1 template visible in "Create from Template..." dialog which is first version. You can delete it, but visually nothing will happen to user. You'll still see "A" template. It will be 2nd version though. If you'll try to import template without making changes - you'll be asked to replace existing one or not.
Thanks for the report - I'll look into it.