If the line numbers aren’t green, it seems like Firebug cannot debug that part of code because it is out of scope. So, if you’re using something like $(function () { … }); Firebug will not be able to access Functions and variables.
Does that make sense?
Also, is it possible that some other function or something is overriding the one you’re trying to debug. It’s even possible if you’re including the same JS file twice.
Hope that helps.