I have experienced first-hand what you are talking about. I have a BS in IT with a concentration in Software Development. I have been a programmer, and a Technical Writer for companies such as Google and Microsoft. Sounds good, right?
Not really. Or maybe I should say, "Yes, and no."
I have been programming since 1983 yet get paid less than men who weren't even born in 1983. I have been lucky enough to work for Google and Microsoft, yet my Google manager told me that he didn't think I was "technical enough" to work for Google even though I know more programming languages than he does.
I am often the only woman in a group, and, as you say, I get along fine with my male companions, and have a great deal in common with them. Yet there is still a disconnect for some reason between my abilities and the perception that people have of who I am and what I am capable of doing.
I try not to be a complainer, but you are right. It is still uncomfortable to join a group and be asked to act as the secretary and take notes.