The problem here is confusion about what symptoms chlamydia does and doesn't cause. When you had it initially, you mention burning when urinating. That certainly can be caused by chlamydia. However, chlamydia was the direct cause of none of your other symptoms at that time. Neither chlamydia nor any other STD causes changes in the testicular skin, cloudy urine, or scrotal sweathing. Even the uncomfortable urination wasn't necessarily due to chlamydia; you might have had asymptomatic chlamydial infection plus some other cause of the remainder. Other than urinary burning, the other symptoms do not sound like any infection at all.
So I'm not at all surprised that when the same symptoms recurred, you didn't have chlamydia and the antibiotics made no difference. I would have suggested the possibility of a prostate problem, but that seems to have been ruled out. Nevertheless, you might do some reading about the chronic pelvic pain syndrome, which used to be considered a form of non-infectious chronic prostatitis -- although the prostate gland itself probably isn't involved. Google CPPS (spell it out) for lots of good information; especially see the excellent Wikipedia article and the information you'll find from the Stanford University department of Urology.
In any case, you can rely on the test results: Regardless of similarity of some symptoms, they prove you haven't had chlamydia since the first episode. There is no such thing as chlamydia not detected by the current tests, and there is no chlamydia that is not cured by the antibiotics you have had.
As far as your specific symptoms are concerned: urine cloudiness and color are related primarily to diet, fluid intake, and urine volume. (Next time you have cloudy urine, collect some in a clear glass and add a few drops of lemon juice or vinegar. Most likely it will immediately turn crystal clear. That's because most cloudy urine, related to diet, is due to phosphate salts that precipitate [become visible] in alkaline urine and dissolve readily with more acidity.) As far as variations in the appearance of your scrotal skin, has a health care provider carefully examined the skin? Did s/he confirm the skin was in fact different than normal, or is this all in your perceptions?
Whatever is going on, I suggest you just stop worrying about it. All of us get unexplained symptoms involving various parts of our bodies, whether it's back pain, headaches, abdominal pain, shooting pains here and there, and so on. There is no reason to suppose the genitals are immune. Since multiple medical evaluations have turned up nothing important, you can be sure that you have nothing that will ever harm your health or that of a sex partner.
It might be smart to have one more visit with one of your providers, whichever one you related to best and/or seemed most knowledgeable. Discuss my perspectives and see what s/he says. (You could print out this reply and take it along.) If s/he agrees with my assessment, you can move on without worry.
Best wishes--- HHH, MD