Thank you everyone for your replies and words of encouragement-- I felt pretty down after that messges, so your positive responses did truly help.
Cup o'Joe-- thank you for your message as well. This program was in my field. With my phrasing there, I was just trying to indicate that some of the strongest schools in this discipline (at least, as far as the standard field specific rankings go) had accepted me, while this institution was indicating that I wasn't qualified to enter a PhD program without remedial work. Of course, any ranking system, should be taken with a grain of salt, but many people may see a difference between schools like Berkeley, UCSD, MIT, etc., and a smaller regional university. While certainly not all of the gradcafe results postings are accurate, my gpa and associated scores were at least a full std. dev above that which I looked at that were posted for this school. I have double majors in chem and EE and both have all of the requisite course work for PhD programs, though I only applied in one field. This is why I felt many of his choice of words were so hurtful, and I truly just did not understand.
I do not think my gender plays a role at all in the response sent to me by the director (if I did-- that would be a completely different story). What I was trying to convey is that I think it's right to tell *anyone* that s/he is unqualified or can't follow simple instructions (as he inferred about the deadline), when that is not the case. In a field like EE where women earn far fewer PhDs (asee puts it at about 17%), I think that's especially a bad idea if you're trying to recruit women to the field-- which may or may not be the case for a department.