First off, clearly you had it turned up WAY too high. A sub should never stand out and when setup properly will hardly be noticeable until a serious boom occurs in the soundtrack. If I were you I'd start with calibrating the thing before assuming you cannot use it.
Second, room resonances are a real thing and without addressing them with acoustic treatments (which entails installing somewhat large bass traps and resonators) you can often remedy things by moving the sub and/or listening position. There are dozens of methods for finding the most ideal placement, but my favorite if the sub is light enough is to put the sub on the listening position seat and playing a test tone (pink noise) then crawling around the room where there is space for the subwoofer so your head is near where the woofer would be and just listening for the least boomy location. After a hour of that, if your significant other doesn't call the funny farm for a pickup, you will know what to listen for and have a good idea of where place the sub. If you want to move the listening position, do the same with potential seating locations while the sub is in the best place otherwise. This is a pretty effective approach.
Third, acoustic treatments are far better at remedying room resonant problems than just about anything else. A large bass trap in one or more corner would help, as would a resonant panel trap (I have three in my HT). These either take some education and work on your part to build and install yourself, or you can buy them from any of dozens of great suppliers. GIK Acoustics is one of my favorites in the more affordable category.
Fourth, as a last resort you can use a notch EQ filter to just take out of the subwoofer signal any information at the specific resonances of the room. This can be helpful, but it also means never hearing those frequencies even when you should (like a synth note at that specific frequency in an EDM or Rap style song). Some receivers have advanced auto-tuning algorithms to program these filters, or you can buy a processor and program it yourself. Doing so would require some measurement tools, so if you are buying those anyway, you can use them to also improve placement and even improve the overall sound of the entire system.
That's my advice.
Additional potential issue to address... it is entire possible that the perception of resonances is caused more by the crossover range needing tuning where poor crossover adjustments have caused the range in the one to two octaves around the crossover frequency being cancelled out and suddenly below that range the output is robust and strong. Properly tuning a crossover isn't always easy, but it can make a world of difference. Heeman and I spent half a day tuning his and found a happy middle ground between perceived performance and measured performance, and we were using a calibrated mic, RTA, and test tones to do it. It makes a difference.
Cheers!
