Antibiotics are apparently HARD on their natural gut bacteria. My vet won't even use them unless they stop eating, loose weight, etc. Mine was going through the same thing. He said as long as she was eating her pellets and veggies, fruits, etc. to let her fight it off on her own so long as no downward spiral happened, but she was around the 4 week mark at the time, and he thought it could be risky. She seems more sensitive to bedding than a male I have in another cage that never seems phased by anything; but switching to 100% Aspen worked for her (she was sneezing a lot prior, her breathing sounding like a tiny diaphragm drum moving). Fleece, I think you need to be careful with the clothes detergent as there could be allergies from perfumes, chemicals, etc. which might even be present on what you are wearing.
She still has trouble wheeking correctly though, in that her whistle is either ABOVE 16khz (meaning I can't personally hear it as 16khz is roughly my cut-off range at 40 years old) which would cause it to only sound like wind I think, or if their tongue against the back of their teeth is required to actually wheek, she might not be physically able at the moment or teeth gap/spacing might tight, etc. (pure guessing here but possible); I can mimic the same wheek sound spot-on (I've fooled pet store employees out of sight that come running thinking something is wrong) and can get my male pig going with it, but for me it requires tip of tongue to the back of upper front teeth, pressed firmly against the gum line, while doing a pulse of air in-mouth. At times, I've had difficulty making the sound, and instead get "air" only, which is exactly what my female sounds like at the moment. I have heard her wheek "weakly" early on, but as of late, I only hear her making the wind sound.