You got a good handle on it Jim. Different amps have different sound. This is why pro audio guys think we are crazy. But the output transistors all sound different, as do their circuits. Cables, well, you know the deal with that.
Rolling off at 48Hz means they are -3dB at that freq. Sealed means they roll off at 12dB per octave, so they are only -9 down at 24Hz. In addition, the room, especially a bass bowl like concrete basement reflects some (or a lot) of that bass back into the room and boosts the bass by 12dB/oct with dropping freq, matching the driver rolloff. You can get flat FR as low as you want if you choose the right diameter bass driver to match the size of your room. Seems like you got it about right with the 10s.
Definitely run a couple more sweeps of the room in different places. If you see that 90 Hz peak not going away or changing freq then you know it's coming from your system, not the room. When you move the mic the room modes will rise and fall and different modes will make other freqs come up and down. When things stay the same despite moving the mic, then the EQ is being played into the room. If you find that it is a room mode or combination of them, the easiest thing to try since it is only 10dB bump is to move your speakers around. Measure once to establish baseline, then move them 1 foot forward toward the listener and sweep again without moving the mic at all. If that changes the bump significantly then you can work on positioning the speakers. I recommend trying the Master Set procedure. It is described well on Audiocircle by Stephen Harr. It works pretty well to flatten the bass response.
http://www.audiocircle.com/index.php?topic=64320.0http://www.audiocircle.com/index.php?topic=65908.0If there's any chance you think the extra bass could be coming from the system, you should try applying EQ, as an experiment, to see if things get better. The easiest way I know to do that is to install trial JRiver, and play some tunes through their parametric EQ module. You should be able to measure the room on the same computer while playing tunes from JRiver, but you'll know by ear if it's working.
You can rip a couple tracks to the hard drive, play them through the headphone jack to your preamp. Hifi doesn't matter here, we're just thinking about the rough bass EQ which will be close enough through the PC. Any headphone jack will be well within 2dB correct FR.
You have mentioned aversion to applying EQ, but if the system is making the bump, then there is already EQ in the system and you are just correcting and removing what shouldn't be there. I agree that Behringer DEQ2496 shouldn't be in anyone's audiophile system, but there are many other ways to get the job done that don't hurt the SQ at all. Jriver and omnimic together will help you figure out what actually works, before you make a corrector.
What is the width of your woofer front baffle? Did you apply baffle step correction before your bass to mid crossover?