"Mountaineering" boots

I have hikes in all seasons but not a great deal.  I have ice climbed for 2 seasons.  Recently I've purchased some "mountaineering" boots like LaSportiva Nepal cube, boreal cerro torre,  and asolo north (in blue).

 I find these hard to walk in but I see how they would be good to ice climb in.  My question does the sole break in because right now I walk like I have 2x 4's strapped to my feet.  Or is it that they would flex fine if I had a 60 lb pack on?  I don't see how the stiffness helps me hike .  Any insights to share?

I'm absolutely no expert on boots, but my understanding is that mountaineering boots often have a full shank that allows the wearer to edge with the toes, and holds the foot flat with crampons. Which makes them a poor choice for hiking in. I believe some boots come with a 3/4 length shank as a sort of compromise between mountaineering and scrambling, but are still fairly uncomfortable for just hiking.

No, the sole doesn't get more flexible over time (at least it shouldn't). As you've already figured out, you need to have a stiff sole if you want to use crampons, unless you're only doing easy glacier walks.

The sole should never flex on the La Sportiva Nepal Cubes.  There is a ridged shank running through them actively preventing this.  The most flex that will ever come will be from the ankle area, and this should not flex particularly more than when they are new.  

Full shank ridged sole boots are not intended for all-season hiking.  They are intended for kicking steps into steep snow and kicking crampons into solid ice.  

It sounds like you are using these boots for the wrong purpose - in which case you'll just hate your very fancy boots.  You may want to look at more burley trekking boots rather than mountaineering boots.  Lots of people love the Asolo Fugitive GTX.

If you are looking for a general mountaineering boot that also hikes well, look into the La Sportiva Trango Cube. The Trango Cube has a 3/4 shank so it works well with crampons and kicking steps in snow slopes, but it also hikes well. I own both the Nepal and Trango Cubes. The Nepals are my go to boot for technical ice/alpine stuff while the Trangos are for more general trips and hikes. Both boots excel at what they were designed for. Just make sure you get the right boot for your objectives.