I think that girls and boys do think differently, but sometimes the "problem" with this is not the kids' differences, but the teachers' inability to think/explain things in more than one way. (The old "it's my way or it's wrong" issue.)
I say this from personal experience, as a student and a teacher. When I was an undergrad, majoring in physics there were 35 of us in the freshman class, 5 were females. We had to take a problem solving course, basically to be taught how to analyze and solve scientifically written word problems. Every problem set we turned in was graded by 1 of 2 prof's and then he met with you and discussed your work, how you did, what your errors were, how to improve, that sort of thing. Once I arrived for my discussion session to find 3 of the dept. profs there - all to discuss and analyze my way of thinking! (Talk about intimidating crazy ). This ended up being the first of many discussions over my 4 yrs in college with the profs about the different approaches their female students took when solving problems, designing experiments, and completing labs. Through these conversations it became really clear that there was a definite difference between the way male and female students were approaching/solving and investigating physics. I was amazed and intrigued by all of this and began noticing how we interacted with each other and how the guys in my classes approached the problems and explained them versus how the females did.
It was similar in graduate school - the guys always thought differently than I did about almost all problems we had to do. It was only when I met my first female physicist and she actually understood where I was coming from and how I approached things did I begin to believe that there really wasn't anything wrong with me or my way of doing things.

Now, as a teacher, I see it all the time, whether I'm teaching middle school math or science or higher level physics. My male and female students explain themselves differently, often times quarreling with each other over a problem when they are actually saying the same thing, but can't see it from each others perspective.

I do not think that these differences mean that one is better than the other, and I do not have hard, empirical evidence to back this up, but I see the differences and see how those differences lead some teachers to react and act differently to boys and girls.