Form alter in a custom module
If the part of the form you're altering doesn't exist when you're altering it (if it's put there by some other form-altering module) OR if some other module is altering the form after you and wiping out what you're doing then you can indeed have a module weight problem. The way to find out is to put a dsm() (see devel module) in your code and see what the form looks like before your alter. Or use a debugger of course (recommended!)