I have been successfully using FSX-SE with the PMDG 737 and 777 aircraft for some time now without any issue of key and control assignments which were set up through the FSX . Recently I wanted to add a joystick controller simply to operate the rudders for ground steering but having left a few previously set up assignments to that joystick, I found it messed up all my settings for the aircraft and so I disconnected the joystick. Unfortunately when doing that it completely removed or rearranged my existing settings and I had to then reset all settings from scratch. Each time when I thought I had it right and exited FSX-SE and shutdown the PC I found when restarting FSX all my assignments were messed up again. This has happened 3 or 4 times. Each time I saved the assignments via the Save option on FSX settings front window but still no joy. Can anyone please advise how to properly save my control/key assignments for all my PMDG aircraft so that they reload automatically each time I start FSX-SE? I do not have FSUIP installed and I am operating on Windows 7 - Pro.

Many thanks,

Mark.

This is FSX boxed, should be similar.
Just a hunch, perhaps try starting FS with admin privileges : 
Right click .exe --> properties --> compatibility tab --> change settings for all users --> check - run as administrator.
The xml file that hold the assignments are in C:\Users\<username>\AppData\Roaming\Microsoft\FSX\Controls -
maybe something happened to your system, unbeknownst to you, that prevents writing back to the control xml file.