If you've found that you can't edit Cata beta/alpha MPQs the way you used to, then try out the newest version of Ladik's MPQ Editor.
Pros:
-Updated to allow patch editing
-New UI features
Cons:
-Some old .MPQs may not work, keep your old version just in case.
Download:
New and Old
The newest version can be found here.
This is for people who want to edit cata MPQs but have issues with small errors, this was NOT made by me, I just want people to know that there are higher versions of the MPQ editor out there.