I also managed to get it to work in my navbar template, the set up I have is follows.
Custom template called cvr4_search profile, this is called from withIn the navbar template using the raw code, I then have a hook which calls this template and it shOws just fine.
Inside the cvr4_searchprofile I need to place the notification code to show new notifications, it's here where it's not working. So notifications need to be working inside a custom template which is called from within the navbar template.
Does that make sense?
Thanks for your testing, it's very mug appreciated.