In the W3TC Cloudflare extension - Performance>Extensions>Cloudflare - Settings, once the checkboxes for Flush Cloudflare on Post Modifications and Exclude minified JS files from being processed by Rocket Loader are checked, and save all settings, those settings are not saved and the checkboxes remain unchecked.
In the Performance>General Settings, under the Exclude minified JS files from being processed by Rocket Loader section the Flush Cloudflare on Post Modifications checkbox can be checked and settings saved.
In the W3TC Cloudflare extension - Performance>Extensions>Cloudflare - Settings, once the checkboxes for Flush Cloudflare on Post Modifications and Exclude minified JS files from being processed by Rocket Loader are checked, and save all settings, those settings are not saved and the checkboxes remain unchecked.
In the Performance>General Settings, under the Exclude minified JS files from being processed by Rocket Loader section the Flush Cloudflare on Post Modifications checkbox can be checked and settings saved.