The solution is to move the application back to the visible screen and then remember not to move it to the second screen in the future. This is a bug in the application since 99% of applications check to confirm that they are restoring their windows to valid coordinates before restoring.
What you need to do is this:
1) Press <ALT><TAB> to select the invisible application
2) Press <ALT><SPACE> to select the application's menu
3) Press M to select the Move menu item
4) Use the arrow keys to move the application's window back to the screen where it'll be visible.
The direction which you need to move the application's window depends upon how you set up your secondary screen. Generally the secondary screen is to the right of the primary screen and, in that case, you would simply move the invisible application window to the left using the arrow key in order to see it with the primary screen.
Multiple screened computing is very productive, I'd say that two 15″ screens are better than a single 21″ even though the single 21″ has more pixels.

