Try adjusting the phase relationship of the subwoofer to the mains. Could be sub is substantially out of phase and cancelling at various frequencies in the low octaves. While there is no exact solution either physically or in time (phase) in a room where there are thousands of reflections you may be able to minimize the cancellation and create a better overall balance. To "see" what is going on I recommend using a spectrum analyzer, preferably one with constant percentage bandwidth filters, 1/3 octave minimum or 1/24 octave is better. Very narrow band usually labeled FFT spectrum is also useful but can get confusing. There are a number of free programs out there that work great for analyzing room acoustics. Below is a link to some of the best I have found. I think you will enjoy being able to see a little bit of what's going on and correlate that with your subjective impression. Once you get a picture of what the room and speakers are doing you can try some of the many corrective solutions that are available. Let us know how it goes.
https://listoffreeware.com/free-audio-spectrum-analyzer-software-windows/
https://listoffreeware.com/free-audio-spectrum-analyzer-software-windows/