It doesn't sound like you are doing anything wrong, but I do think you are unnecessarily feeling a bit defeated! Although I should imagine you feel like this at the end of all your DSD's visits, and then have to steel yourself for the next time...
It also doesn't sound from what you have described as though your DSD is behaving in an abnormal way, given the circumstances. Or are you concerned that she may have mild special needs? (ie are you genuinely concerned that she can't really help her behaviour, or that it tips over into being abnormally manipulative and needs professional attention, or are you just frustrated that she is difficult to live with for a few days a month?).
I know I certainly wouldn't have appreciated, at 11, having to leave my local friends and family, and creature comforts, every school holiday for a few days, to spend time with a father I loved but didn't know very well and a stepmother who was well meaning, but, obviously, wasn't my mother, so unlikely ever to love me warts and all. I would particularly dislike this if surrounded by a generally poisonous family atmosphere where some members of the family were so angry with my father that they wouldn't even speak to him. I would feel very confused and angry, not really knowing how I was supposed to behave or who I was supposed to express approval or disapproval of, and would be hypersensitive to even the slightest hint of disapproval or criticism. And however patient you try to be, there is no way you will have been able to completely conceal your feelings - that you don't really believe she has much wrong with her eyesight, don't believe she has genuine food allergies, and don't believe she has problems with her breathing, along with not believing that she could possibly be that incapable of making a few decisions for herself. And if she is aware that you are dubious about these things, then who is she supposed to think you are feeling critical of - her mother, or her, presumably?
In other words, whether you are right or wrong that she seems to think there is an awful lot more physically wrong with her than is actually the case, you don't really see her often enough to be in a very good position to cast judgment, meaning that if you do, you will not be thanked for it, even if everything you do is intended to be in her best interests.