Running my application from visual studio debugger

If I lauch my application and run my script eveything works great. When I launch my application from visual studio the script mouse button presses no longer work.

I am using the script to debug a software issue so I want my application to be started from the debugger. I ran the AU3recorder to try and help me figure out what was going on and none of my application button presses show up in the record results when launched from the debugger.