What version of Windows, Vista or Win 7?
Is the problem that it starts minimized, or that the window is not visible, i.e., if you click the taskbar button, does it open? Or can you see it move off screen? (click the button repeatedly, see if you can get a glimpse)
Does the same thing happen if you use the start menu shortcut at All Programs | Accessories | Command Prompt?
If it's not visible, it may be positioned off screen. If Win 7, click the taskbar button so Command is the active window, then press WinKey+RightArrow.
This should snap it to the right side of the screen. Click and drag the title bar to position it on screen.
Or right click the task button, then right click Command Prompt, then click Properties.
Click the Layout tab, uncheck "Let system position the window" if checked, then set both boxes under Window Position to 0
If Vista, right click the task button, then click Properties.
Click the Layout tab, uncheck "Let system position the window" if checked, then set both boxes under Window Position to 0
You can also try to right click the taskbar button, then click Move, then use the arrow keys to move it back on screen. If you can't see which direction the window opens, you'll just have to experiment.