Unmapped ports usually indicates that one audio interface (the hardware, like a Steinberg UR824 or RME FireFace) has been substituted for another. Cubase configures itself for the inputs and outputs of the last interface that was used. So when a new un-configured interface appears, it tries to map the inputs and outputs to the new interface.
The best solution for missing ports: Without a Project currently loaded, go to VST Connections (in the Devices menu) and configure the Inputs and Output settings for your particular audio interface. (Unless you're using a multi-output configuration, you'll only need one stereo output buss defined in the Output tab.) For example, I've attached a screenshot of my Input settings. With this configuration, I can record from all 16-inputs of my Steinberg MR816CSX interface.)
Once you have the configuration setup properly, I'd recommend saving presets for both the Input and Output settings so that you can recall the setup for any loaded Project.
For more information, you can view Tutorial #6 from Cubase 6 101, Tutorial #3 from Cubase 7 103, or you can access your Cubase Elements 6 manual by clicking the Help menu, then selecting Documentation, and choosing Operation Manual from the list.
[url=http://www.macprovideo.com/forum/upload/upload/server/php/savedfiles/files/mpv_44432_93591_Screen_Shot_2014-08-11_at_9.39.34_AM.png] [img]http://www.macprovideo.com/forum/upload/upload/server/php/savedfiles/thumbnails/mpv_44432_93591_Screen_Shot_2014-08-11_at_9.39.34_AM.png[/img] [/url]