Just wanted to throw my issues into this thread. Same permalink problems combined with SEO Yoast.
I have installed the latest WP version, 4.0 as well as the latest Enfold at this point.

I have talked to the support at Yoast that recommended the following which I have tried to flush out were the problem is:

The latest WordPress update may have caused issues with your other plugins which probably created a conflict with ours. Please try deactivating all of your plugins except the Yoast plugins and switch to a default theme like Twenty Fourteen. If the problem goes away, activate your plugins one at a time and check if the issue comes back for every plugin activated. Finally after all plugins are active, switch to your theme and see if the problem is resolved. This will narrow down the conflict to a specific plugin or a theme conflict.

So I did. All plugins was deactivated except for SEO Yoast with Enfold and it screwed up the permalink. I activated a default WP theme and all worked fine. I changed back to Enfold and the problems started again – no other plugins in action at this point. Seem like the problem is in Enfold somewhere?!

Hope there is an fix for this since I really don’t want to change my SEO plugins – and I need it badly for our business.
Have a nice day good people :-)