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It's either black algea or mold. Without sunlight I don't know if algea will grow.I believe one of the byproducts of MPS is phosphates which algea LOVE.Also with your not using chlorine the spots may be the results of it - something decided to grow.
Chad, I use Chlorox Clean up.. since it is chlorine based. I don't know what is in Tilex, it may be sodium Hydroxide..so check that first. The Chlorox works great even for cleaning my tub when I do a dump and refill. I just rinse it out of the tub. I think on the cover you could just scrub and wipe off. good luck
Chad,I wouldn't worry too much about the stabilizer. Any and all of us that use dichlor have high CYA in a month and really high in 3 months. Most people who own pools use trichlor and their stabilizer is probably through the roof as well. Remember that every time we add 1 PPM chlorine we are ading 0.9 PPM CYA.Chlorine is still killing bacteria at 300 PPM CYA although it doesn't kill the hot tub itch bacteria. Instead of changing completely why don't you modify your current way of doing things - maybe add chlorine 1/2 way through your week instead of MPS and see how that goes.As far as cleaning the cover, I usually only use bleach and water and let it sit a while on the cover. I do notice that anything that resembles mold ( I sometimes get a pink substance on my cover) takes a while to disappear completely.