I can think of only three reasons for a statement like that.
She's a damn good interviewer and she decided to put you on the mat for a 'stock answer' to see how you dealt with it.
She doesn't have a clue what your skills mean. Programming in C is very different to programming in java, sort of ignorance.
She saw the bulk of your technical skill set as irrelevant, linux in an MS house type of thing.
So her response to which would give you enough material to 'prove' different and or be a good reaction to her initial challenge.
Course I'm sat at home, in an interview, my face would have crumpled and I would have started blubbering at the unfairness of it all. :D
I would hope that it was reason one, could live with three, two, she'd have failed, I don't work for eejits who 'know' what they are doing.
I'd want to know who gave her the facts too, I don't mind people talking about me, even if they say unflattering things, they should at least have the bottle to do it to my face though.
Anyone who gives you an unofficial reference without mentioning that they have, is usually some sort of twat.