I solved removing the plugin & the theme, reinstalling the theme & (don’t know why) saving the mobile.css file in the editor.. by the way it is a truly strange behaviour.
For some reason the plugin doesn’t like the media queries in the mobile.css file.
For others experiencing this, you just need to deactivate the auto minification and then clear the cache. There shouldn’t be any need to re-install the theme.
Then you can manually minify the files you want, excluding the mobile.css file.
I’ll spend an hour this weekend trying to figure out why this happens (only sometimes).