I think it’s very unlikely that you accidentally changed this shortcut (could be done in the User Preferences). I guess it’s a bug. Sometimes it happens in my projects that the y key and the z key are interchanged and I haven’t got an explanation for this behaviour either…
You say that the a key works in other projects. What I would do (maybe there’re better ways) is to open a new project and to append your scene…
Go to the Select menu in the 3dview header, and see if the shortcut is still behind ‘select/deselect all’. If not, right-click on it & ‘change shortcut’ or ‘add shortcut’.
Even when other functions have ‘A’ assigned to them, I don’t think they can override the default one