Could be a vwm issue. You could try !vmwgather in an lsxcommand. Or...

Try this:

1. Open a window - don't maximize it, so it's out of sight (your problem).

2. Assuming the newly opened window has focused, hold ALT and press/release SPACEBAR, then press/release M, then release ALT.

Your mouse cursor should have vanished at this point. It will be centered over the window's caption bar (which is off screen), and have changed to the cross-arrows cursors.

3. Press any arrow key (up/down/left/right) for about a second and release it.

Now the window should be attached to your mouse's movement.

4. Move your mouse around, until you hopefully see the window.

That's about it. Then you can try closing the window and reopening it, to see if it's saved its new position.