your speakers are distorting. i bet your crankin your stereo up to hear the subs, then the speakers seem to be cutting out. set your HU's eq to get the sound right so they dont distort. this will only minimize the problem.
ideally, you would want to replace all the speakers and run a 4 channel amp. you would notice a huge difference.
See it is in a bmw and the bmw has a stock alpine amp for the highs. and i just ran wire from stock amps remote wire and spliced it into my kicker remote wire so i wouldn't have to run two wires. and there is a built in EQ and crossover on my deck, and i have them set for just highs and mids.
my car also has a factory amp, and between the factory speakers and amp its just not powerful enough when you add subs to the system. the subs either drown out the highs, or you have to turn it up so loud that the highs start to distort.
aftermarket speakers and amp would greatly enhance the sq of the system.