I found this article:
It hints that running the execution server as a process instead of a service might help.
It also says that "Run Exclusive" might help.
But you should be careful about using "Run Exclusive" because allowing only one monitor to run at a time is quite a restriction.
We saw a same issue and suggested the following :
The script was launching the application by double clicking on the desktop icon. So it was not getting launched via TM ART Central because this method behaves differently through terminal services.
So instead it was replaced with a more robust method of starting the application which involved launching from the main executable.