To apply your registration, start All My Movies and select menu item "Help - About".
Click on the "Register..." button and enter your activation code.
You have to be connected to the Internet for the proper activation.
Could it possibly be installed to two different locations? You mentioned that you downloaded the program twice.
You could try uninstalling the program and rebooting before attempting to reinstall.
If nothing else works, open AMM and from the toolbar select 'Help' > 'Support' and request help from the developers.
I'm sorry that you are having a difficult time right now. Please don't give up! I have personally purchased and test driven several different movie organizer applications, and AllMyMovies (even with its' occasional quirks) outperforms them all. You will tweak it to your own preferences as time goes by.