It sounds like a problem with the amp tuning. Maybe the gain is set to high on your sub.
If you had it professionally tuned, make sure it is tuned at flat response. If it sounds too boomy at flat response, then your amp isn't tuned properly. Also, different people tune amps differently. So, maybe you need another amp tuner to tune your amp.
It sounds like a great system though. You can't go wrong with JL products.
Also, I would make sure your speakers are in phase and check the balance and fade. For example, if you set balance left, do you only hear the left speakers? If you fade rear, do you only hear the rear speakers.
Sometimes the installers mess those up. If any of these are wrong, including phase, your system won't sound right.