Good questions. Cloudflare has minify enabled, W3TC has it disabled. W3TC does have 'rewrite URL structure' enabled, though.
In Cloudflare's CDNJS-section, Modernizr, Flexie and JSON2 are on.
By the way, I just noticed this message, written in red on the top of the W3TC settings page:
It appears Page Cache URL rewriting is not working. If using apache, verify that the server configuration allows .htaccess or if using nginx verify all configuration files are included in the configuration.
I did have some problems with the .htaccess file of my WordPress-folder last week (got a 500 Internal Server Error after messing with a referrer group in W3TC and solved it by renaming that .htaccess). Maybe W3TC is behaving strangely? Should I try removing and re-installing it?
Roibn
