Toward the bottom of the window, there is a "Show options" link that opens a set of options that you can change. One of the available options is "Left partner" whitch you can set to male or female. I don't recall what the default is, but maybe flipping this back and forth will fix your problem.
Is this a general problem, or just when there are multiple partners? I ask, because on my trees the females are always on the left unless there are multiple partners.