JBL monitors on ISO pads.
So I've got the following:
JBL 306 (6.5" woofer) monitors on ISO-130 stands
Axe FX 3 on the latest firmware
Friedman Small Box model with default settings
York Audio 2x12 Creamback Mix 01 IR
It honestly sounds fine without any cuts on my end. I'm checking the RTA coming off the Amp/Cab and there's a natural roll off happening a little over 100 Hz. If I add in the cuts around 80-100 Hz it controls the very low frequencies a little more. York Audio impulses have less low end than many others I've tried in the first place, I can often run minimal cuts on the lows, then cut the highs to taste.
Only two things I can think of:
Try changing the slope of the low cut to 12 db/octave or even higher, that can cut off more of the low end. You can try bumping it up closer to 100 Hz or even a little higher depending on the slope and how it sounds.
You may want to experiment with monitor placement in your room. If you don't have sound treatment, it's very possible you could have some wave reinforcements causing a big bump in the low end.
I was frustrated with my monitors a few weeks back and picked up a reference mic for $40 to measure the room. It turned out there was a big bump at around 150 Hz and then huge dips above and below it which screwed up the low end. Also one speaker measured different than the other due to placement. I ended up rearranging the room to sit against another wall and the low end issues smoothed out quite a bit and there was more L/R consistency.