This experiment rocks, by the way. I'm looking forward to the next several months' eggs. It takes me back to my Biochem lab in college. We took old (over a year old) eggs and did a bunch of tests on them, then extracted the cholesterol from the yolk at the end. I don't remember them smelling bad or looking any different than any other eggs, although I wouldn't eat 'em.

If you get a bad one though, it may be a fluke. I would bet that, because the shell is porous, some stuff may have gotten through the shell before it got to the jellied stage. Great experiment, keep it up!