Can you let me know if you have any other caching plugins installed, such as WP Supercache or WE Total Cache, etc. And who and what hosting package your using. This is usually caused by having those types of plugins containing cached versions of the site after Autoptimize has been cleared. Normally that clears all of your local site cache files, not just Autoptimize.
If you use a host that uses their own server side caching methods it can also cause this. The extra info may help me pin down exactly why that’s happening. Also, I’ll finally have an updated version of the plugin out by the weekend, and it will save the settings as soon as it’s installed, which should solve this.
Apologies for the issue. Thank you for reporting it.