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If I open the binds file with notepad, I can see that all my keybindings are there. I've checked it while playing and they show up in the notepad even when in game all the fields are empty, I've tried setting the file to read only as well but nothing changed.
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I have a suggestion for you to test and see if we can work out what is going on:
Move all the files from %LOCALAPPDATA%\Frontier Developments\Elite Dangerous\Options\Bindings directory - every one - to another location.
Start the game - go to options and select Keyboard and Mouse from the drop down list (this should work with any of the default presets).
Move down to change any setting at all (or several) then click apply - (the name in the drop down has changed to custom).
Exit the game.
You should now have a brand new Custom.3.0.binds file in the above directory (and also a StartPreset.start file).
Now load the game again - see if your custom binds has loaded and if the changes you made above are there.
I have literally just carried out the above steps to confirm it works ok (new StartPreset.start and Custom.3.0.binds were written by the game).
If not - then I am at a loss completely as to what is going on.
EDIT: The file "BindingLoadingErrors.log" was not created by the game - whether it will create this if there is an error in future I don't know - I moved my previous file back after checking the game loaded correctly the new custom binds above just in case (it is an empty text file im my case).
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