Many Thanks for your help!
I have updated the utility MFDWindowTest.zip (should be version 1.0.0.2)
Please download, extract the EXE into the MFDCougar folder and run (Elite doesn't need to be running).
Press the
LOAD button - it should display MFD #1 and MFD #2 windows - on the monitors and in the correct positions.
If the windows are not correct, reposition them and then click
SAVE button. This will update the MFD.ini file (you should see the update if you carefully read the info panel).
You could then close/reopen the utility, or click the
LOAD button again and see if the windows are behaving.
It would be good to see a video of all of this if something is going wrong. It's hard to see why something should be wrong, because this is all basic window stuff and nothing out of the ordinary is occurring.