If you've tried other equipment exhibiting the same problems then that would point toward setup I believe. Are speakers placed along the long wall as should be, or are you incorrectly firing into the long dimension of the room? However there may be other factors at work; I'm wondering about your cabling? Interconnects, speaker cables, AC cords; many are not neutral & then when they work together the overall results can become even less so. You might already know about these techniques, but I'll briefly review just in case.
My own approach is to go for neutrality regarding interconnects & speaker cables, then do my tuning with upgrade AC cords. Every AC cord sounds different; you'd be surprised at the changes in tonal balance that can be accomplished by experimenting with different AC cords on different components. Others also like to tune with interconnects & speaker cables, which does work but also adds more variables into the mix which can be very confusing trying to figure out how everything is working together. Of course these cable issues also all interact with your specific equipment & the whole synergy issue then becomes even more clouded. That's why you can have a rig that's tuned up very nicely, & then changing any one of these variables really messes the whole thing up.
Mark above also mentions resonance control, which could be very important esp. in this case where a specific frequency band is really acting out. This resonance behavior could be related to floor movement, your equipment rack, the room, etc. Look into component isolation & vibration control which is a whole 'nother subject altogether. Cones coupling speakers to the floor or to a shelf could do a lot of good here. I really wouldn't be blaming the amp & speakers etc; you have some good stuff there.
My own approach is to go for neutrality regarding interconnects & speaker cables, then do my tuning with upgrade AC cords. Every AC cord sounds different; you'd be surprised at the changes in tonal balance that can be accomplished by experimenting with different AC cords on different components. Others also like to tune with interconnects & speaker cables, which does work but also adds more variables into the mix which can be very confusing trying to figure out how everything is working together. Of course these cable issues also all interact with your specific equipment & the whole synergy issue then becomes even more clouded. That's why you can have a rig that's tuned up very nicely, & then changing any one of these variables really messes the whole thing up.
Mark above also mentions resonance control, which could be very important esp. in this case where a specific frequency band is really acting out. This resonance behavior could be related to floor movement, your equipment rack, the room, etc. Look into component isolation & vibration control which is a whole 'nother subject altogether. Cones coupling speakers to the floor or to a shelf could do a lot of good here. I really wouldn't be blaming the amp & speakers etc; you have some good stuff there.