I found this thread really interesting, as an editor. I've worked for small/medium independent publishers for many years, but started my career in a big house.
I can only speak for myself, but I've experienced gender bias and plain old sexism from the marketing side of publishing far more than the editorial side--a greater willingness to increase promotional budget for male authors, an irrational focus on the marketability of female authors based on sex appeal etc.
I have never worked with a male editor who shortchanged women, or vice versa, that I'm aware of. Perhaps I'm lucky or just unobservant. But I agree that bias can be unconscious.
My present publisher is heavily into technology, and submissions are swept electronically for (among other things) repetition, plagiarism, reading level, and keyword strings. They get numbered so that they are read in order of receipt. Author names are removed from files sent out for reading.
Some readers are really peeved by this and want to know the writer's gender, like strangers not sure how to react to a baby unless it's in pink or blue. That seems to bear out the idea of unconscious bias.
It's also my experience that women re-submit with less frequency than men. I've often provided encouragement and constructive comments to a woman, and...silence. I can count on one hand the number of men who didn't try again.