You *should* only have one cable between the system and monitor; either VGA or HDMI. As to your issue, I'm going to take a wild guess and say that your monitor is currently displaying the VGA output which your computer is seeing as a secondary/extended screen. Your primary screen is the HDMI output of your graphics card. I'd be curious to see if your desktop appeared if you switched your monitor from the VGA input to the HDMI input.
Either way, just connect one cable (recommend HDMI) from the graphics card to the monitor and it should resolve the issue.
-Wolf sends