Something Katy linked to reminded me of this test (Are there two female characters who talk about something other than a man?), and the stories I've written actually don't do very well at all.
Graveyard Shift, Recursive Herbology, and any fanfiction.
OK, this doesn't really count because I'm using Pratchett's characters, and the interesting ones are Carrot, Vimes and the Patrician. If I were writing about the Witches, there would be nothing but female/female conversations, but I have three male characters. It's not my fault :)
Slash, including Mablung/Damrod and the Good Southron.
Again, somewhat handicapped, but a couple of female characters have been the viewpoint.
For instance Alaheda, while the MDaGS never quite made it to the final revision, had a clear image in my mind, and while she fancied M/D, that didn't matter to who she was. Her main drive was her brother, who she was overshadowed by in Southron culture, who could as well have been a sister if the Southron prejudices were against something other than women. An original character with, you know, character. This is good.
Maurice Saldini, Gothique Investigature.
Dinah is Maurice's friend. A priest, generally wise, calm, and tolerant. I liked her very much, but in retrospect, she is defined not as an individual character but as the character Maurice needed to be friends with. People reading early drafts said they barely noticed her at all. (NB: This was written before I met Angel :))
A bit part is a member of her choir whose missingness, and extremity of religion, drives the plot, with whom Dinah has a relationship, though it barely shows.
The only other major character is the rat narrator, who I thought of as male, in true buddy movie tradition, but from a human perspective it doesn't really matter, but I suddenly realise I'm not sure if I ever refer to him other than "it" and "I"?
Flewt and Gerald
Again we see the problem that my main characters are always men. But this is what I can write, nothing else works.
There are nine councillors of the City of Diamonds, with whom I played musical genders. The two most prominent are men, because their position in the plot had become fixed, but for the others it didn't matter, and several came to life when I switched them female-to-male or vice-versa.
And, in Eisvale, a lesbian couple. Ice started as a small character provided for Gerald to talk to, but took on a life of her own and stole two chapters of the story. Her estrangement from Seaflake, and relationships with the other Magi of Eisvale define her, though she quickly develops a wry friendship with Gerald.
Cissy
The story explores Cissy's personality, his platonic relationship with Natalie, and how those are affected by meeting Sean and the Boss, so Cissy, Natalie and the boss's genders and interpersonal relationships are fixed, and Cissy is definitely male.
Sean is the viewpoint. Actually, it would change the dynamic with Cissy a bit, but Sean *could* be female, and he is friends with Cissy.
Usgietha is a bit part female, but she and Natalie never meet because of the plot, and because a lot of the story is driven by Cissy, so we see interactions with him more.
Conclusion
I have a tendency to make characters, major and minor, male by default, counteracted by a reflex to ask "Could this character be different?", and find it difficult to switch later, or to invent female main characters.
But then, all my characters are male geeks with a laconic humour and tendency to perpetrate gratuitously gothic phraseology, because they're all exactly like me! :) I think that is the root cause, I'm still having lots of fun exploring variations on the theme, and haven't really had any really different characters.