FSX:SE and FSX Running Missions disables 2D Main Panel

I recently decided to update from my trusty FSX to the Steam Edition because of the opportunity for improvements and support that getting onto the Steam platform would mean and that a lot of people were enthusiastically endorsing.
I expected, because of my Triple Monitor situation, that I would have to redo a number of previous customizations to 2D panels, mostly consisting of inserting window size and position attributes into each panel to get them to scale properly.  I did about half my aircraft inventory using free flight mode to test the changes which all came out pretty well in Free Flight.
But then I tried to run some missions, Resort Supply and Africa Relief speifically
What happens is this:

1. Start FSX:SE

2. Select Free Flight and choose any of the aircraft whose panels had been corrected - perfect!

3. Select a Mission - only tested with Africa Relief and Resort Supply so far.

4. 2D Main Panel doesn't display - but all other 2D panels can be selected via SHIFT-N commands (2,3,4,5.....) and display correctly - but SHIFT-1 on toggles between a 1/2 screen vertically and a full screen verticall with no instrument panel showing.

5. End Mission and select Free Flight with same or different aircraft - 2D Main Panel no longer appears but all the rest do - just as with the Mission.
6. Exit FSX:SE
7. Start FSX:SE

8. Select Free Flight and choose aircraft - 2d Main Panel appears as normal

In summary then:  If I do Free Flight everything works correctly but if I run a mission then all 2D Main Panels disappear and cannot be restored without shutting down FSX and restarting FSX.

I suspect it has something to do with the mission mode using that cueing window - whose scaling parameters I haven't been able to find yet - or some change made by the mission to the overall screen coordinate system.  But so far, I'm getting nowhere.

Does anyone have any hints or areas I should focus on either in the .FLT files of the FSX.cfg file?