Just say you don't want to do it? I understanding that painting someone else's nails, or having your nails painted for you, can be very romantic/intimate (under the right circumstances; right time, right place, right mood ~ lighting, hehehe ~ right person most importantly I think) but if this is the only way you can be intimate together, something smells bad and it's not the nail polish.
I'm sorry - that may have been too blunt. Don't say THAT to her, whatever you do! What I'd do is, well, you can ask her why it's important to her. Don't sound accusatory when you do. I mean, you can just do it, this once, and ask while you're doing it, 'what is it about this that is different when I do it as opposed to you painting your own toenails?' - or words to that affect, if you don't speak like that. I have a very stilted language style, I think. Don't talk like that, if you don't talk like that normally, she'll know something's up. And then try to figure it out from there, or - well, tell me what she said, I'll try to help, if I can :)
I like to think I'm good at understanding girls; being a girl, who's been around mostly other women my entire life (same-sex schooling; mostly women in my household, my friends are almost entirely women) and most of my more meaningful relationships have been with women. Or maybe I'm just being bigheaded aahaha :)