My wife has the same problem. I've been lurking for a while trying to find a solution, as we've tried on dozens of boots over the past month with no success.
She currently rides a size 6, and we've gone all the way up to a 7 in the hopes of taking the pressure off her instep to maintain some circulation. No luck. Either the pressure is too much for her to take, or if not, her feet go numb within about 2 minutes standing the shop anyway. We've tried different insoles, her boots have intuition liners that we've molded and remolded, and we've been to several shops to try to fix the issue. No luck.
Finally we were able to get an appointment at our local shop with their top boot fitter, and after studying her feet and trying to understand the problem, we confirmed that her 3rd metatarsal sticks up higher than the rest, which of course subjects it to significant constant pressure, which then affects her circulation.
First we got her out of her current un-articulated boa's and into a Forum Mist, which has regular laces and an articulated cuff. It was a size 6, but had a bit more toe room, which was good. But, the instep pressure was still there, and worse than her current boots.
He removed some foam from the liner tongue to create a pocket for her bone, which I've heard of other people doing, and which helped a bit, but he also heated up the tongue of the boot SHELL and bumped it out into sort of a dome shape on the instep area, similar to how you'd do a ski boot. It took a couple tries to get the shape just right, but once it was done, it was like a whole new world for her. She stood wearing them for 20-30 minutes with zero pressure and zero numbness. This was all with the stock footbed.
The last thing he did was to mold a custom footbed for her, which made things even better, but I don't think was absolutely necessary to solve the numbing issue.
Of course, the true test will be on Sunday when we head out to test them out. But just from wearing them around for a bit, she is confident that there is a 1000% difference. I should note that this was also a size 6 boot, which is exactly what she measured and exactly what her old boot was. No need to go up in size to fix the issue, and her heels stays put exactly where it should.
If your fitter won't do this, find one who will. Most of the ones I talked to would only mold a foot bed and try to heat mold the liner, neither of which worked.
Oh yeah, one more detail . . . the cost of the custom work was $60, the footbed was $150. Expensive, yes, but the owner of the shop spent 3 hours with us, past their closing time, and made it so my wife can actually take more than one run at a time. Well worth it if you ask me.