This phrase originated with the advent of vans as common vehicles. There were two seats in the front, and then nothing but space in the back. Most van owners outfitted the empty area with shag carpeting and enormous pillows, making it something of a "love nest." As a result, a very common phrase (and bumper sticker) was "If the van's a-rocking, don't come a-knocking."
Meaning that if a couple was involved in an act of intimacy, the van would be rocking back and forth with their amorous movements. If you happened to see a parked van that was bumping up and down thusly, then you should not disturb the occupants. The phrase has since been adapted to indicate any area (apartment, flat, etc.) where a couple might be having sex.