I downloaded the file and I briefly looked at it. I already see where your error is but i will go in depth with it tomorrow. but just to start you off, your problem lies in the fact that you have the menu animation repeating throughout the timeline at every frame label and this is what is causing your problem. You need to put the menu in it's own movie clip and have it sit at the beginning of the timeline when it animates in. You can do one of 2 things. You can create the buttone functions inside that menu movieclip or reference the buttons from the main timeline actionscript.

there are a few other things that you need to change and fix in this fla to have a good working movie.(lots of little habbits you will need to break ) I will write up a list of things and post them for you tomorrow.