Please ignore the second part, I finally understood what was the problem.

For future reference if anyone has the same problem, the problem is that I was making all the slides with transparent background, and adding a background image has a primary layer.
That is why the transitions were not working.
Or better, they were working, but on a transparent background, so it seemed like nothing was happening.

I still have the problem with W3 Total Cache minify of javascript though.
Pretty soon I will be passing trough CloudFlare, don’t know if their option to minify javascript will have the same problem.