[SirAlvarex]

I always fixed this problem by doing the following:

1) While in windowed mode, switch your resolution to the desired resolution (preferably the size of your desktop resolution, or bigger).
2) Position the window so that it covers the entire screen.
3) Switch to fullscreen.

For some reason, if I were to click in any area where the window wasn't present, my program would minimize.

I guess that the client keeps track of where it is on the screen, and doesn't overwrite some value when switched to full screen.

I haven't tried what Aggressor posted. Sounds like it could work.