Here’s my take:
I interpret this as "lower midrange issues" at frequencies that are cirtical to your listening. The lower mid is difficult to get "right" in that we are asking the speaker to be both agile (detail) and powerful (moving lots of air) at the same time. At these frequencies controlling the cone movement during long(er) excursions is no easy task. Frequency response is measured at the factory at 1 watt @ 1 meter, which is at a very low STATIC volume level. Now, introduce dynamic elements into the equation and you may find that as speaker that measured -6 db at 48Hz is far below that mark when high energy is sent to the driver. It may fall well behind the other midrange frequencies and sound "anemic". I call this "pinching the midrange" whereby the bandwidth changes relative to speaker output. When powered subs are added to the system, they are happy filling in those deficient frequencies abandoned by the midrange and can become quite dominant. This produces sonic "warts" that will not only bring attention to the subs, but the subs are not as good as the mains in producing detail in those areas.
I did a quick search for your speakers and appears that ATC makes some pretty nice stuff. The spec you mentioned of -6db @48Hz is interesting in that -3db is a typical published spec. -3db represents the point where HALF of the energy is gone (it would take twice the power, or twice as many speakers to flatten it out). That’s pretty significant. -6db is 3 db below that point, so your missing half again as much sound at that frequency. Not seeing a graph, I can only speculate at this, but it appears that you COULD have compromised lower midrange at 100Hz, or even higher. That being said, it’s not a matter of what frequency instruments change from music to sound, but rather your speaker’s ability to produce BOTH detail and acoustical energy at those frequencies. This task, then, is handed over to the subs (and, depending on the sub) may, or may not do a good job of sending the signal out into the listening room in good shape. The room could be a factor here as well.
I’d try turning off the subs and listening to your mains full range at moderate volume levels to see if the lower midrange musical detail, body and richness are there. If so, it’s a matter of dialing in the sound of the subs for best sound quality (probably subs set lower than you have them set currently). If these sonic elements are missing, you may want to do some speaker shopping.