I know this post is old but in the event you or any one else is looking for an answer, I found a manual work around and/or solution in my case.
If you have Netflow enable on your Network devices and exporting it to prime.
Navigate to Services > Application Visibility & Control > Data Sources
From the Data Sources window you will see list of devices that are exporting Netflow to Prime. If you know at least the source router for the unknown traffic, you can do the following.
Click the "I" or information icon next to the Data Source, then check the box for the "Raw Report"
Now, click the Netflow hyperlink in the Netflow Template column. this will open the Netflow Templates window, click the "Launch Report" hyper link in the upper right corner.
A new Netflow Report is opened, click the DataSource for the router or network device, select a time period, report title, etc, then click run and/or you can save the report as new template.
The Report Run Results will be displayed in the next window and you will have a full view of the raw traffic including source destination IPs and Ports.
Now, this will at least give you view of the traffic, but you will still have to determine the unknown traffic but it easily down by correlating source and destination IPs, time frames, etc and or just by know the applications and traffic on your network.
You can then go to Services > Application Visibility & Control > Application and Services and create and add the unknown ports, and/or services.
Not a perfect answer or solution but it helped identify and label most of our custom apps and traffic not known by Prime.
