It seems to me you actually turned down the overall volume of the sub. You really need to get an SPL meter and calibrate properly. I suspect you have the sub too "hot" or loud.

With the rumble you hear on those scenes, or other scenes, what is the volume like on the rest of the system?

By using the gain control on the sub, you should try to get the receiver to just a few db above zero on the sub volume.

Bottoming out happens when the excursion of the driver exceeds the limit and hits the structure behind it.