Ask what she's doing

"A-HEM!" I cough, leaning on the door frame with a crooked grin. "I assure you they're quite clean, Naoto. I'm sure there's no need to subject them to such a thorough examination."

"Eep!" I had never heard such a high-pitched sound out of her, and the flush of her cheeks as she whipped around, still guiltily clutching my boxers. "Uh...John! I...erm...I mean, of course they're clean. That's uh, not what I was doing. I was...detecting! Seeing if I could deduce, uh, well, anything..."

I had to restrain a laugh--it was so delicious to see her flustered! I crossed my arms and shook my head.

"Come on, now, Naoto. If we're going to be living and working together, than we need to be open and honest with each other. Now are you going to tell me what you were really doing or not?" If she did, it would hopefully help her a little out of her shell. If not...well, maybe I should demonstrate a bit of 'deductive prowess', helped by the fact that she was programmed to my specifications?