In some ways I am kind of the opposite of No_iD - which is why I have coined myself the label GGG (gender gifted girl) to describe myself.
In my case I absolutely identify as female - but now that I am comfortable with my own body I find that I also "get" the male stuff as well. Which is kind of odd because I never did when I was...

So with me it's not a case of not fitting in with the girls - I can do that just fine, it's that there is more of me, and I can also hang with the boys just as easily. In a sense I can feel like one of either, according to whom I'm with. Being just one is too restrictive.
But to answer the question of how I realised, that happened when I started coming to this site and realised that I didn't "get" some of the very gender polarised attitudes that many MtF and FtM people seem to have... For example the male and female privileges lost and gained threads... I know they are all in fun - but the vehemence with which some people disect those threads really shocked me.
I suppose it's natural that if you are having to fight for your right to be a certain gender you may tend to also try to become an ultra version of it... but then I never really had to fight - so inevitably I have ended up somewhat more fluid and relaxed about it all.
Am I an Androgyne? I don't know... but I guess I feel that as I have a lot of symapthy with the attitudes of the folks in this area of the site, so even if being a GGG is a slight varient on the theme, I guess it must fall within the broad and inclusive Androgyne definition.