Certificate Assistant swaps extension settings for CA / Users
So I've been looking into this further and from what I read here and there, I am pretty sure that it is not supposed to be doing this. I have reported this bug to apple and if I ever get an answer from them I will update this post.

If anyone with the same problem finds this post, this is the temporary solution I used:


Create the certificate authority and for any extension that gives you two screens enter the same values in both. Those should be the values you want on the certificate itself.
When done, go to ~/Library/Application Support/Certificate Authority/[ca name] and edit the template file there for the values you actually wanted to enter into the second screen of every extension.