I have never heard any of my male colleagues referred to as "boy" 
I have, however, heard / been the target of lots of examples where women (yes, middle aged - our office avg age is about mid-late 40s) are usually referred to as:
"the new girl"
"the admin girl" (woman who's retiring in the next ten years - don't know her exact age but she's certainly not a girl)
"the phone girl" (our receptionist)
"who's their girl?" (meant as our primary contact for a project)
etc.
Personally, I don't think the people using the term mean anything nasty by it. And I think we do have more important things to worry about, such as lack of equality of opportunity in the workplace (my sector, too).
But that doesn't mean to say it's not patronising.
Or has any place in a professional environment in 2011.
It essentially links "women" = "less mature/respected/infants" vs. men, where "boy" would sound very very odd - I'm not doubting people here have offices where it's used, but actually if I'm being honest maybe the reason why I've not heard it used is because of the racial implications? We are heavily involved in the charity/NFP organisations - perhaps there's a rub off there?
Because let's face it, a white male manager in his 30s calling an early 40s black employee "boy" continually wouldn't be acceptable, because of the connotations involved (showing a lack of respect, etc) - just as it does, in a more subtle way, for women deemed "girl".
So, OP, YANBU. It's a silly thing to write in a professional email in 2011, but I'm not surprised, unfortunately.