Hmmm, just a wild guess, but I would start by excluding "cart.min.js" from JavaScript optimization.
Alternatively (if you're up to it) you could just exclude /checkout from being autoptimized using the autoptimize_filter_noptimize function of the API. This is documented in the "autoptimize_helper.php_example in your Autoptimize folder (the 3rd example).