I was having the same issue and came to the same conclusion for the cause. For me to get around it I use two different LUAs.
One is for "Multi Monitor" and used whenever the export is required. FA-18, A-10C etc. On top of the monitor is MFDs and Buddyfox.
The other is "Single Monitor" used for flying Helicopters such as UH-1H, Gazelle etc. All I do it turn the second screen off but still use the MFD / Buddyfox on top as button boxes.
If you like I can send my two LUA files as it looks like you have the same resolution across your screens as I do.
Hope this helps.