Which version of Duet Web Control is it running? Look in the Settings General page to find out. The latest version is 1.22.4.
Thinking about this more I wonder? If I change the config file and reload the firmware without power cycling the board or force reloading the Web interface, what are the chances I would get some of the behavior I was seeing? What determines the button actions, and can they get out of sync with config.g?
BTW, I believe the default micro stepping when I installed the board was 16 for XYZ and 8 for E. With this as a starting point it's likely things went off the rails for reasons I didn't grasp at the time. There was definitely a period where the web interface was not in sync with what config.g was set to. And it persisted through reloading and power cycling because it happened of the course of several days.