MacBook Air :: Apps Don't Appear Properly In Dock

My friend's MBP was doing this recently, and asked me if I had a solution - to which I did not, and now my MBA is doing this: 

On the left side of my dock, I have all the applications I frequently use, Finder, Browser, Mail, etc etc.  And on the right side of my dock, ive put a few folders for my documents, applications, and downloaded items, for quick access to them. 

My other applications, when openned from the Applications folder on the right side of the dock, would usually pop a little icon down on the left side of the dock, indicating that particular application was currently running, and where you could click on it - view files currently openned, that sort of thing.  And now - That no longer happens?  When the app is openned, it no longer puts an icon on the left side.  Theres no presence that the app is currenly running.  If i have several apps running at once maximized, I can no longer Tab between them back and forth, or click between them on the dock.  And when I minimize the app It no longer receides into its icon on the left (because the icon doesnt appear there anymore), but now minimizes to the right hand side of the dock. 

I don't know what has changed, or happenned, and I doubt it's something I did - because I rarely mess around with the settings on this thing.  It operates perfectly otherwise.   

Info:
MacBook Air