I think one of the differences is that women are not so inclined to ask for more money. I spent years not asking for a pay rise in one job I had because I was too embarrassed (STUPID). See this article (http://news.bbc.co.uk/2/hi/business/4195852.stm) which states that Female British workers earn on average 27% less than their male counterparts. It states that 66% of women were too scared to ask for more money, compared to 24% of men. Thank heavens for proper transparent pay scales.
As to whether women are paid less than men for doing the same job, there have certainly been some high profile employment tribunal sex discrimination cases in the City where women have fought and won settlements because they received lower pay or bonuses.