I have many thoughts on this interesting topic, and I hope that I can crystallize them here without offending anyone. Everyone has a unique history, and everyone - whether male or female - is different. While knowing that generalizations can be inherently dangerous, we nonetheless find patterns while examining our experiences, and we learn what tends to work for us in relationships.
I'm one of those women who has a more difficult time getting along with other women. I don't identify as a tomboy, either. I'm still very aware of the social and biological differences between myself and my guy friends, and while I can relate to them at least better than I relate to women, I know those differences will always be present. With female friends, however, I have often struggled to maintain identification at all. There are several reasons for this, and the negative experiences of my adolescence have almost certainly augmented the interpersonal distance on some level.
My elementary, middle, and high school years were, for lack of a better word, horrible. The bullying began when I was in first grade, and while some eras were worse than others, it remained a consistent factor throughout my childhood and teenage years. This torment, whether by coincidence or not, was perpetrated exclusively by the other girls. When I was six years old, I couldn't understand why this was happening; I only knew that it was, and that it hurt. It began with name-calling, social exclusion, etc., but soon escalated to the theft of my personal property and the orchestration of pranks intended to publicly humiliate me. I knew a completely different group of girls by the time I reached high school, but things had not improved much. I regularly received hate mail, which dissected and ridiculed my personality, sometimes outright encouraging me to kill myself. I began to spend most of my time in the counselor's office. Sometimes I skipped school when I couldn't work up the mental stamina to endure it. Eventually, I ended up in professional therapy. I had one loyal friend, and yes, he was a boy. (We are still friends to this day.)
I've been able to do a lot of healing in the six years between then and now, but I'm still a little wary of new women. It's not that I immediately dislike them or have no desire to befriend them; it simply takes more time and effort to build trust and become comfortable around them (as compared to men). At the same time, if a woman complains about difficulty or drama with other women, I will not dismiss her. There is always a chance that the issues could be very serious, and she may be in great need of someone to talk to.
Okay - now I need to move away from the heavy stuff.
I think people tend to forge closer relationships over shared interests, tastes, and experiences. Most of my tastes and interests are not stereotypically feminine. I'm not remotely suggesting that all women like romantic comedies, makeovers, and gossip rags, but I personally don't care for any of those items and therefore should not be expected to prefer the company of someone who is a stereotypical girly-girl. It has simply been trickier to find female buddies who enjoy the same things I do. Again, I'm not saying those girls don't exist; I just haven't met them, and it has consequently been easier to connect with guys over these activities. One of my guy pals couldn't get a night off work when we had planned to go to a hockey game (for which I already had tickets), so I dragged a female friend along instead. It was a bad experience for both of us.
Then there's the matter of clashing perspectives. In particular, my views on relationships and sex tend to contrast quite a bit from the opinions of my female friends. We can still get along, but it's hard for either party to discuss certain issues without raising eyebrows or making the other person feel judged in some way. Again, my guy friends actually empathize with my perspectives more often than not.
And yes, there are absolutely differences between a man-man friendship and the friendship maintained by a man and myself. Sometimes the relationship does indeed shift from platonic to romantic. We're both adults, and these things can and do happen. It's nobody's fault. In fact, this is just about the only way I can cultivate a meaningful romantic interest in someone - by being friends first. My boyfriend and I were friends for about six months before we acknowledged our chemistry. On the other hand, it can be difficult to discourage a friend you're not interested in, or to swallow feelings when they're not reciprocated. With a strong bond and mutual respect, however, this doesn't have to be insurmountable.
Gender role fulfillment crops up every so often too, which serves as a reminder that I'm not "one of the guys." One of my friends is a total bro on the surface, but he always looks out for me whenever we (and a couple of other male friends) go out for drinks. He tends to watch when other guys approach me, and steps in if they behave inappropriately.
Ultimately, we all bring individual personalities and experiences to the table, and not all of us are going to prefer the same things. I've unfortunately had to make some generalizations in order to illustrate my viewpoints here, but I believe that gender is not a neat, clean, black and white concept. There are girls who enjoy sports and men who care about fashion, girls who dislike talking about their emotions and men who can't get enough of it. I'm only reporting what has been true for myself, so that I can explain why I seem to prefer the company of men.
tl;dr: The expression of one's frustration with other women need not necessarily be a sign of misogyny, immaturity, insecurity, projection, or low self-esteem. To automatically dismiss it as such seems lazy, in my opinion.