To make the theme persistent over game updates, find or create the file GraphicsConfigurationOverride.xml inside your home directory under the (possibly hidden) directory %LocalAppData% (Windows) or Library/Application Support (OS X), and there under the directory Frontier Developments/Elite Dangerous/Options/Graphics. The file can be used to override any settings found in GraphicsConfiguration.xml, but for setting the HUD theme its contents should be:

Code:

<?xml version="1.0" encoding="UTF-8" ?> <GraphicsConfig>     <GUIColour>         <Default>             <LocalisationName>Standard</LocalisationName>             <MatrixRed> 1, 0, 0 </MatrixRed>             <MatrixGreen> 0, 1, 0 </MatrixGreen>             <MatrixBlue> 0, 0, 1 </MatrixBlue>         </Default>     </GUIColour> </GraphicsConfig>

This example is the default HUD theme – replace the Matrix lines with the code snippet from the editor. You can undo the modification either by using the above code for the default theme or removing the entire GUIColour section from the file.

I had this same issue playing directly (not under steam). I had migrated my controls configuration to a new PC, and had mistakenly copied the custom.binds to:
C:\Users\[user]\AppData\Local\Frontier_Developments\Products\FORC-FDEV-D-1010\ControlSchemes
Make sure you do not have a custom.binds file in this folder. The custom.binds file belongs in:
C:\Users\[user]\AppData\Local\Frontier Developments\Elite Dangerous\Options\Bindings