Why are my dock applications turning into question marks after restarting my macbook pro?

So i have had my new MBP with retina display for a few weeks now, and everytime I shutdown or restart the computer, I have a bunch of question marks in my dock instead of my application icons. The question marks still show the name of the application under them, and after I click them they turn back into the proper icon. I noticed that they are only applications I have installed myself off the internet. It never happens to the applcations that came with my macbook, or apps from the mac app store. I have not moved the location of the applications i installed, so i dont know why the computer is having trouble displaying the icons. I am new to the mac operating system and am wondering if I may not have installed these applications properly. The apps that are constatly turning into question marks include Bittorent, VLC Player, PS3 Media Server, Air VIdeo Server, and the Dolphin gamecube emulator. I have looked all over the internet but i cannot find a solution. Please Help!

When they go grey, it means that they have lost the location of the application that they represent.
If you put your mouse over each one, it will tell you what application it is that it has lost.
Go to wherever you have that application stored, usually the applications folder, and drag the icon of the application down into the dock. A new icon is created for you.
Repeat with the other two grey icons in the dock.
To remove the grey icons, left click and hold while you drag the icon out of the dock and onto the desktop. Release the mouse button and the icon will disappear in a puff of smoke.

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