CSS & JS minification operates on cached CSS and JS files only. Once Cloudflare returns a cache HIT for the file it will be returned to browsers in minified form. This allows us to deliver a more complete minification result. If you need to enable or disable minification for CSS & JS you will now need to purge your Cloudflare cache to see the effect of any minification change.
The Auto Minify option can be found under the Speed app in the Cloudflare dashboard:
If you encounter any issues with Minification, check out our article that explains why Minification may not be working.