Have you tried running a compressor upfront in the stomp section?
If there's one prevailing range of freqs you can arm a parametric eq, set a tight range (high values of Q), set the gain to maximum and slowly sweep the freq till you find the boominess is exagerated. Then invert the gain to minimum.
HTH
Other than parametric EQs, you might want to try to re-record those bass parts and mute the strings with your picking hand to avoid them from ringing out, which really accentuates the boominess.
post processing for bass in general - look for boomy frequency and notch it 5-10db usually at around 133hz.
Also helpfull: multibandcompression, dialed in that it controls these zones and the lowend when a boomy note comes
And don't forget to check if it is just your room!!!
play a commercially released CD. Does the bass seem boomier in the room than it does other places?
And, what are you using for monitor speakers?
Does the Kemper output LED hit a higher value when you play these notes compared to adjacent ones?
If it does, it's not the room. Guitars have their own resonant frequencies, that's not unheard of. Your electric likely has a tendency to resonate around 224Hz and needs the same treatment if you chug a lot.
A surgical EQ is a good on-board fix. A multiband compressor is better, but not on-board.
I have a suspicion it could be the room - easy ways of telling?
Plug in headphones. If the boom is gone it's probably the room.
You could use a signal generator playing sinewaves at different pitches. If a sinewave at the same (more or less) pitch of your basses "boom notes" is significantly louder it's very probably something in your room (the room itself, speaker placement etc.)
most likely the room and/or placement of the monitors.
How far away are your monitors from the rear wall? Are they placed in a corner? Do you have some kind of foam pads that de-couple your monitors from the surface below?
This depends on what range of frequencies is most boosted, reflecting surfaces have few to do with low freqs actually: it's more the size and shape of the room itself. No ise to put carpets or "egg boxes" on the walls 
As for the pads, I use Mo-Pads by Auralex. Keep in kind tho thst they will just kill the resonances deriving by the mechanical coupling of cabs and desk, and if the latter have no role in the resonances you're hearing, you'll get no benefits for the specific issue (but the overall sound will benefit nevertheless).
Absorbing bass is much more difficult than absorbing other frequencies. Good luck
No ise to put carpets or "egg boxes" on the walls
just to clarify:
putting carpet or eggboxes on the wall will NEVER help a room.
carpet makes the room sound muffled and egg carton kills only a very small frequency range, like a notch filter.
both are a really bad idea.
What do you recommend for the walls? Our rehearsal room has no coverage on the walls, just the stones. Everything else but carpet would be very expensive, I think.
See, treating a room is a matter of measuring and determining its sonic personality. The behaviour on the low frequencies basically depends on the size and proportions of the room itself, while the behaviour of longer wavelenghts depends on the surfaces. A pattern with peaks and valleys such as an eggbox, for example, kills the frequency whose wavelenght corresponds to twice the difference between the valleys and the peaks, like Don pointed out.
Basically, you can't treat a room a priori, as if there was a magic treatment good for any kind of resonance or dampening. Once you realize where the non-linearities are through a (even rough) battery of tests, you'll be able to make a decision about what to put where or what to remove from the room.
HTH
Thanks Gianfranco. I've expected an answer like yours. There seems to be no universal way that leads to an acceptable compromise.
You're welcome
Nowadays, javing a sinusoidal sweeping from 20 to 20,000 Hzon a ny computer is... free There are also downloadable collections of synusoidal tones, or CDs.
If you are curious, run a slow sweep in your room through your monitors and see what happens. You'll hear many peaks and valleys, and it can be funny, useful and educational at the same time. Just be aware that you'll hear the sum of your ears', the room's and the monitors' non-linearities and, above all, that what you'll be hearing depends on where in the room both you and your monitors are placed.
Another very interesting experiment is to settle a fixed synusoid, and move through the room: you will litterally cross the peaks and valleys created by the room's resonating modes, which is amazing per se; and will realize that certain reinforcements or dumpings just take place in precisely spotted aread of the environment, depending on where the waves sum or subtract from each others.
