I did a lot of research on this one and found several people with a similar issue, but no correct answers, so I figured I would post my solution.
Issue: I received my new Cubesim MFD and hooked them up. When I added the Cubesim lua it did not work. This lead me to download and configure my viewports with Helios 1.6. This work great to get the viewports using the generic MFD left and MFD right onto the Cubesims, but when I jumped into my trusty F-16C the backgrounds on the MFD were transparent and showing the clouds and ground as I flew (see photo of Cubesims). After hours of troubleshoot and endless Google search's I realized what has happening on my setup. I had my monitor setup to the top right of the main screen (see attached red frame drawing). What the view port was doing was displaying an extension of the main screen view similar to using multiple monitor setups where you want to see more of the world to the left and right of the main monitor.
Solution: Simply relocated the Cubesim monitor to the bottom of my main screen and redoing my monitorsetup with Helios. Now everything functions fine. I also switched to the Helios F-16 patched viewports. This affected the location of the viewport from the original location with the generic MFD viewport.
I seen in other post that people were have an issue with the alignment of the view port in Cubesim MFDs so I will share my setup using Helios 1.6 to help.
Main monitor 3440x1440
Left MFD 800x600
Right MFD 800x 600
Helios setting for both MFD
600x600
left 90
top 0