Could be an unusual shadow pattern, an area with cold air (eg under loft access area), or some odd-sounding echo.

As it's very particular areas at particular times of the day, I would think it would be a light/shadow pattern he dislikes, thinking he may fall into something or there is a step he can't climb.

FWIW, electronic toys can go off at random times if the child drools enough to mess with the electronics.