Program running, but no where to be found? Mac OS X 10.6.7

Situation: I'll click the application in the application folder, it will load (like normal), it will even show up in my dock, and the top bar even shows up with all the application menu bars. However, the program itself is no where to be found. So far, two of my programs do this.

I'm not running spaces, or any sort of parallels, I've updated my software, I've tried force quitting and restarting (both application and computer). But, nothing works. The program still opens, but is invisible.

My computer is a macbook pro, Mac OS X 10.6.7 with a 2.7 GHz Intel Core i7, and I also go back and forth with using two screens via a HDMI chord. HELP!