Windowed mode not showing up suddenly

[DystopianFr33k]

Alright, I have a Gateway NV79 laptop with a Core i5, a Mobility Radeon HD5650 1GB, and 4GB of DDR3 RAM. I have been playing Zelda OoT on a plugged in Flatron W2340V 23" HD Monitor. Suddenly, the game crashed, which wouldn't be a big deal, except now when I open Project 64 and select the ROM, the game won't appear unless I hit escape and go into fullscreen. I have tried changing the windowed resolution, and it has not fixed it. I have tried restarting the computer, and still nothing. This did not happen ten minutes ago, only after the game crashed. I can hear the game running and if I hit alt+tab I can see the program there, and the game running in it, but it doesn't show up on the actual desktop, even when I set focus to it. Disconnecting the external monitor doesn't change anything.

Edit: The computer is running Windows 7 Home Premium

 

[Alunalun]

On Vista I know that I can extend my desktop onto an external monitor, drag a program window to the second monitor, and then unplug the monitor, and from then on when I try to run the program the window always "appears" on the now-nonexistent other monitor. Even if I close and re-open that program, it tries to display on an output device that doesn't exist, and the OS doesn't realise.
It may be different with window 7, but I would try rebooting with the monitor plugged in, rebooting without it plugged in, and even plugging/unplugging it while the computer is shut down.
One of those generally works. Forcing re-detection of monitors at all stages might help too.

Or if you are a windows whizz, you might know a way to make it forget the window location settings (or whatever it is that makes a program re-open with the same window size and location as when you last closed it, you know how they do that? I hate that.).

 

[Allnatural]

While PJ64 is running, hit Alt+Space, select Move, and use the arrow keys to reposition the program window.

 

[Alunalun]

That's genius. I always wondered how you selected the window-location menu with ALT.