it seems to me that when -kun is applied to women it is usually to indicate that they are "one of the guys"; like maybe a member of a work group. I have the impression it's a sign of acceptance. Perhaps there is a joking element in there as well.
When -chan is applied to guys there does seem to be more humor behind it. It can also be a carry forward of a childhood nickname into adulthood. Pre-school age boys are commonly addressed with -chan (usually a contraction of their first name plus -chan, e.g. daisuke might become dai-chan)..