I would have to assume the CEO difference is just down to age and generation. If women have only really been considered for those positions for one or two 'generations' of business, many likely don't have the same web of connections (especially including mentors) that men do (even a man from the same family, like an older brother).
I'd expect this to significantly even out with time, but only if women actively pursue (and are encouraged to pursue) positions which are likely more difficult for them to attain (for the above reasons). For this reason, it seems (to me) still necessary for women (especially experienced business women) to promote the idea of women in business, encourage pursuing those careers, ect.
As to the XXcents/dollar, that's going to be debated until the end of time. From completely personal, anecdotal experience, my wife started off as an intern in the company she just finished working for. In that time she was hired and worked her way up over two years, but the person in charge of her department, while a nice guy, just seemed to never get over seeing her as 'that intern girl' (and it's the girl part that sticks, as he doesn't have the same attitude with other former interns, even younger ones). She recently decided (on advice of someone leaving the company) to look for a position elsewhere, and was blown away to discover that other companies were willing to bring her in to a higher position for a significant raise. Now she's bothered she didn't leave to pursue this earlier, as she is now not as far along as some of her fellows of the same age and education (and thus makes less cents on the dollar to them, despite doing the exact same job).
It should be stressed that her previous company was in no way backwards/old time boys club (it's founder is gay, they have many women in high positions), but just that one little attitude held by one person in the company above her has likely contributed to her falling into the 'does the same, makes less' group (though I highly doubt she'll stay there for long).
I feel I should also point out that she managed to get that job through a mentor who was a business woman. Connections are again incredibly important in the professional world.