network settings not honouring bypass proxy

When you say "works fine when I set those rules manually in Firefox but not when I set them under network settings" do you mean Firefox ignores the settings in network settings? Does Safari correctly use the ones in Network Settings. If so I suspect the fault lies with Firefox and you have no alternative to use it's own settings. Such is life with not-quite fully Mac native applications.

Firefox doesn't obey the system-wide settings. Safari should.

There used to be setting in about:config in Firefox, but it seems to be un-implemented and no longer there in Firefox 3.6.xx