The same thing happens to me all of the time when using Outlook. I've got two displays at work, and Outlook is on one but often I view individual messages on the other. When I remotely connect from home (one screen), Outlook displays the messages off screen.
Here's what you can do: when you know that the window with focus is off-screen, press Alt-Spacebar, then M (for Move), then use the arrow keys on your keyboard to move the window into view. I advise practicing this once or twice when you have both displays so that you get the hang of it.
Chris
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