could it be, that the sensors are "hearing" each other?
You have sensors at each end of the box, as far as I understand your pictures.
Thats what i was thinking too, you could also just turn one on for 250ms, then turn the other on, just alternate left and right.
depending on where you are measuring you could be getting some echoic noise off of walls, there are ways to deaden this noise or different surfaces that can increase or decrease noise, you can research into.
i did a project awhile back measuring the distance of my head from a computer monitor (for an automated kvm switch). i remember it working like a charm and not having any noise issues.
maybe you have some bats flying around your test area screwing it up?