I know that you probably have looked at the Properties of the shortcut, and ensured that the field, Run, in the Shortcut tab is properly set. There are three options – Normal window, Minimized, and Maximized.
What has happened to me is that my program IS maximized, it is just that I have moved it off screen. If you right-click the button on the taskbar, do you get a Move? Try using your directional arrows and see if you can move it back on screen.