GSX doesn't change any of the FSX default keys, nor it tries to change the Standard.xml file. If you found this has been changed, it hasn't been changed by GSX.
GSX only use the official, standard, SDK-sanctioned way of requesting keys usign Simconnect, it doesn't modify ANY of the default FSX files, and it stores the key mapping configuration it has obtained by FSX in its own .INI file, which is totally unrelated to FSX.
Instead, it's a *known* issue that, using Windows 8.1, the default controllers sometimes change for no reason.
There was already a discussion here a while ago:
http://www.fsdreamteam.com/forum/index.php/topic,10997.msg85017.html#msg85017An user said it was fixed by using a different gamepad, the other user that participated in that discussion didn't came back to report further testing result, so there was no proof this could be related in any way to GSX.
As I've said, GSX doesn't try to change keys directly in any way.
An *indirect* cause, that was discussed in that thread, might just be due to the fact that when you open the GSX "Key mapping" menu,a dialog is being created by an external .EXE, and this is triggering some kind of FSX bug in the assignment.
In this case, any other 3rd party addon that runs as an external .exe, and would allow to remap keys, would probably cause the same problem.
Have you tried to the new Couatl 3 Public Beta here ? Do you see any differences ?
http://www.fsdreamteam.com/forum/index.php/topic,11796.0.html