I would like to thank LeonidS for his help, patience and effort helping us resolve the UNA Notifications issues that we have been experiencing. 

First off the Duplicate Notifications were caused by CRONjob settings on our side, the UNA Notification system works 100%, the fault was on ourside.

Here is what happened, our users were getting multiple notifications, the cause was 2 fold. 

1. Notifications module had not been installed correctly. Lenoid helped us remove and reinstall the module.

2. We had duplicate CRONjobs. This might sound like a simple thing to check and fix. It is, but you need to understand that Every USER can run CRON jobs, so when you list cronjobs with ROOT it looks like there is just on cronjob listed, the same applies when you list cronjobs with user WWW-WEB  you see this: 

> crontab -l -u root 
# m h  dom mon dow   command
MAILTO=admin@mydomain.com
* * * * * /usr/bin/php -q /var/www/mydomain/periodic/cron.php

That means there are 2x cronjobs running, one for each USER.  

You only want to see one CRONJOB, for one USER, and none for the other users. 

Hope this helps everyone else.