Hummingbird acting weird!

I have been encountering some weird issues with Hummingbird after updating to the latest version. I am using WPEngine CDN and caching.

This is what happens:

1. Under minification, even when the CDN option is disabled, some scripts from ClouldFront get imported and make the form in this page - - disappear. This gets solved by clicking the 'Recheck Files' but just for a while before the scripts come back.
2. Minification is showing a different number of files found at a time.