Flash has its components and one of them is the button, is you all must
certainly know that when you press it the border becomes green and all the
other compoents have some green effects. My question is how can I change this
to become the colour that I want? (I would prefer a 50% Alpha Blue to match the
design of my project)

You need to change the theme that determines the components colour scheme.

The following action script will make all components in you .swf have an
orange colouring:

_global.style.setStyle("themeColor", "haloOrange");

I am assuming that there is a "haloBlue" theme as well. ie:

_global.style.setStyle("themeColor", "haloBlue");

The best way to check is to delve into the help section in Flash Mx and look
up something like "component styles" or "customising components". There is
definitely a list of theme names in there somewhere.

Cheers,
Anth