This happens even if you are not using Terminal Services. At least it does if the main window is maximized.
Was the main window maximized in your system?
I can minimize this effect on my system but not eliminate it entirely.
Immediately after the new window is created, I add a step that resizes the main window back to the maximum screen dimensions. You can't use maximize here, but you can use get functions that return the screen height and width in a move resize window step.
Then I use a script to close the new window and include a step to maximize the system to restore windows back to their original state. The result is the main window "twitches" a bit as it snaps down to just a bit smaller than the application window and then closing the new window triggers another "twitch" as the system returns to it's maximized state.
I searched my own known bug list DB, but can't find a reference to this issue. Either my original report predated the creation of this database or FileMaker didn't consider it a bug... The database does include scripts that demonstrate this work around if you want to take a look:
Thanks for the response. Yes, I believe the window is maximised in our system.
I have passed your info back to our dev team so they can work their magic. I'm going to take a look at the demo scripts now for my info...