Well, when playing with headphones the E notes bass response doesn't stand out compared to the other notes. So it clearly must be a bad room resonance...
I am amazed haha I have never even heard of such a phenomenon, but that bass explosion in the room is insanenow i just have to find a way to fix this issue
Try playing a slow sine wave sweep from 20 Hz - 20 kHz (there are some on YouTube; the crappy encoding doesn't matter so much for this experiment) and listen for times when it seems like the volume gets louder and quieter. That ought to give you an idea of how bad the problems might be and where in the frequency spectrum they are most likely to be found.
As for fixes, at the very least you could try moving your set up and listening position in the room, especially if you have your speakers next to a wall or close to a corner, which will amplify the bass frequencies. Ideally you'll need a lot of bass trapping to reduce the effect of the room modes. At the other end of the scale, you'll need a bigger room with dimensions that are multiples of the golden ratio with bass trapping, absorbers at the mirror points and diffusers 
