I started doing that (selecting only one controller as an input device) recently... it helps but the problem is still there...
There's an instrument track, if it's selected while I'm exporting the project, echoes the instrument track above it.
This only happens when it's exporting but if I simply playback the project, it doesn't happen.
Why would it do this when I'm exporting but not when I'm playing the project, beats me!
So, I don't know what else to do to troubleshoot this. I'm really confused by this.