OK, so I did some more troubleshooting and I believe that the issue is being caused by something internal to the World of Warcraft game files not keyclone, sorry for the bad tag.

I was able to run multiple windows from the original files in Program Files but when I try doing the same thing with the additional Wow files I created for multi-boxing the issue starts, and worse without keyclone for that fact. So, I guess I need to try and repair the install files.