Masculain ou Feminain?

(Apologies for possible French misspellings, high school was a long time ago.)

So today at work a very obviously transgendered person applies for a library card. On the application form there are two check boxes, M and F which are mainly used for statistical purposes but are otherwise not particularly important. The only problem is that our computer system forces you to enter a value in the field in order to create a card. Now occasionally it will happen that someone doesn't fill this field out (usually by accident) and so I will typically do it for them. However, in this case, there is no real easy answer as indeed this transgendered person does not choose one or the other: What is a guy to do?

Having a few transgendered friends, I'm aware of the politics here and certainly don't want to ask the patron which gender he/she identifies for fear of starting a debate on the issue. Is there a right answer here? We certainly didn't cover this in training...