How to "undo" config (Changes in config chunk don't work)

I just installed mm and made my first test config, which worked great. Cool stuff. I cleared the whole config chunk to start from the beginning to create my actual config, but my original changes are not undone? New changes to config chuck don’t change anything. Situation returns back to normal after disabling mm plugin but returns back to weird after enabling the plugin, even when the config chunk is empty. I have tried of logging out/in, clearing cache. What am I missing here. I have 1.0.3 installed.