The sentence "I won't be there until September" is perfectly all right. It implies that she is coming in September, but will not be there until then.
I am only familiar with "up till", not the word uptil, myself (American English). "Up till" is a shortened form of "up until", and its meaning is entirely different from "until" -- "up until", and, I assume, "uptil", is something that is currently true and will remain so until the time specified. "I will be there up until September" means almost the opposite of the first sentence, that is, she is there now and will be there until September, when she is supposedly leaving.
I guess someone could say "I won't be there up until September", meaning that the state of not being there is true now and will remain that way until then, but it is bound to confuse the listener. It's not that there's anything grammatically wrong with it, it's just that the original form is so much more common that the latter form is bound to be misunderstood.
But perhaps it is different in Indian, or British, English. Would anyone from those speaking cultures care to comment?