This is late so might be a moot point now. I was able to get this to work as normal with the following steps.

1. DON'T auto startup wow in Keyclone. In the setup turn that off.

2. Also turn off the auto add World of Warcraft windows in the setup.

3. Save these updated settings and close Keyclone

4. Start your copies of wow normally using the game exe.

5. Then startup Keyclone. Ensure that it's not auto adding the wow windows. (the issue is that Blizz now has 2 windows for each copy of wow game exe running, one hidden and one shown)

6. Click the "add" button in Keyclone, then click on one of the wow game windows. Repeat this for each wow window.

7. Here's the tricky part. For each wow window now, Right click on it in Keyclone (where the title and status window shows) then in the menu find Maximizer open its sub-menu and click the region you want for that window of the wow game. Do this for each wow window open. This should get you back to how keyclone was working originally.

8. Test that your windows work as you expected and the swapping works.