A few years ago I went to Japan for a month long holiday. I entered Japan in Tokyo, but flew directly to Okinawa. After a week in Okinawa I spontaneously decided to go to Taiwan for a couple of days since it was so close to where I was. After returning in Okinawa, I was immediately questioned by a customs lady. She even told me to "not do this again". To me this didn't make any sense, because it merely resulted in a two week extension of the original tourist visa of three months. It was nowhere near the end of the one I got when I landed in Tokyo.
Basically what I'm trying to say: There is no fixed point at which customs will give you a hard time. It can be after the first time, but it also might never happen.