Are you running the stock HU?
If not then it could be a dodgy connection on the remote turn on lead, that turns the rear/sub amp on/off with the HU. If it's a stock HU then it could be an aftermaket one was installed by previous owner and they butchered the wiring, and then bodged it to put the original HU back in when they sold the car.
You need to pull the HU and pot a pic of the wiring behind it.
Is it totally random, or when you go over bumps?
You are correct that the rears and sub run off a separate amp inside the sub. If the wiring looks untouched at the HU then you need to check the sub, which isn't the easiest bit to get to.