Yes, I see that. It looks as though Quickscript is parking the window 1280 pixels over instead of at the edge of the portrait desktop. That is a bug; probably one they need to hear about.
In the meantime, restarting Quickscript when you change orientations would fix it.
This AppleScript will do that
tell application "Axiotron Quickscript"
If you are using MacFlip, putting this script in the "on ChangeDisOrient(notebookOrient)" handler/subroutine after the "do shell script fbRotatePath & " -d " & displayID & " -r " & (notebookOrient as string)" line will automatically restart Quickscript after each orientation change.
But that might be overkill.