I had to delete my WTF, Cache, and Interface folders

[traedoril]

Then I got nothin'...

This sounds like something Lax may have to comment on.

That's fine. I ticketed blizzard on it thinking it was something on the wow end but they informed me that if I run a single instance of wow and I get no problems then it has something to do with ISBoxer.

I need to mention also that when I run a single instance of the game I get a different UI than when I run an ISBoxer instance.

Example:

I run bartender and when I have a single instance running I get my bars in the special keyboard layout that I created.
In ISBoxer I get the generic blizzard setup and I have to reset all my bars. It did save though after I did it once so it is recognizing a wtf file just not the main wow one. This applies to recount, omen and the other addons I run.

Is it possible for me to run to instances of wow manually then have ISBoxer reposition and control them?