A quick patch has been submitted to Steam. This just adds a reset button the the color settings in the Options dialog:
If you are on the beta branch, you may have experienced colors getting loaded incorrectly from the application config file. This was caused by some code added for managing Linux float to string conversion in different regions, and has been corrected.
If you need to reset your color settings to the default, just hit the "Reset" button and press OK to apply the settings.