I have this problem as well and this is how I solved it:

play aroud with the window when you can see it and try to get to the windows 'move' command. generally you can do this by hitting 'Alt' then the down arrow. Although sometimes you have to hit left first and/or down more than once, depending on the windows set up. Once you get to move, hit enter and you can use the arrow keys to move the window. Now, remeber the sequence, and when you lose the window simply move it left or right, depending on your setup, until you find it again.

alternatively, I find that setting the second monitor to attached then unattached will sometimes work as well.