I did something like that before.
I was dualboxing with dual monitors on the same PC. After playing, I shut down both instances and reverted back to 1 monitor. Later on, tried to open POL and it opened in the position where it was previously on the second monitor even though it wasn't active.
To fix this, I had to turn on the second monitor and drag POL back over.
Not saying this is your case but it's very similar.
If anything, you could try right clicking on the bottom bar (not Start) and press Cascade Windows. Should line up all windows open.
ill try that now, the last time i started windower i moved XI to my second monitor. (but just to clearify, it didnt go to my second monitor, its way off to the side of my first monitor opposite where my second screen joins it :<)
edit: that didnt work at all :(