It sounds like you may have set an option to automatically evaluate a whole notebook on open? If so I'm unsure what option that is.
Maybe the notebook has "Initialization Cell" set on Cells and when you open the notebook mathematica for some reason does Not ask if you'd like them evaluated; which it should unless opened programatically. So again maybe you have some option set.
you can open a .nb and edit it in a normal text editor, save it, and then open it in mathematica.. for various reasons this is sometimes useful. In this case there may be options you wish to delete if "open special" will not ignore them.