If your subwoofer has it, try switching the power switch from "auto on" to "on." Some movies don't have constant sound going to the sub, so it detects no signal and turns itself off. Then a scene changes and it switches back on - you get a popping noise.
Also, check your crossover setting in your avr to see if it's set too low, again your sub may only be recieving a signal that is very low. Generally, ~80hz is a good starting point for your crossover, but it could be higher or lower, depending on your speakers and personal preference.
As mentioned, check all your connections to make sure they are tight and try a different sub cable.
Jack