Yeah, the multiple keybinds was acting weird for me too. It seems like it may be an issue with the way multiple keybinds are handled by the program. I might have to change it to the system I wanted in the first place to fix this issue, which would be pressing and holding a single key for different durations. Something like 2 seconds holding would turn it on/off, tapping it would activate it if it's on, and holding for one second would deactivate.
For now, it seems like if you go to the .\RecursionTracker\Settings folder and open "ComponentSettings.xml" you can manually change the keybind in there if you search for "Timer" and find the existing bind to change under <Simple name="key" value="D0" /> and <Simple name="key" value="X" />.
What kind of color would you want instead? It was initially made to be similar to the in-game UI but anything is possible.