Wow - I had the identical problem last winter when I switched from shoes to boots (Vasque Breeze model for both). I wondered if it might simply be the change from low to high tops - now there's some anecdotal evidence that the switch may have been to blame. I had never had a similar problem in 30 years, the first 20 of which involved the use of boots rather than shoes. Since last winter, after switching back to shoes and letting the heel heal (!), I've had no further problems.

I'm planning to try the shoe/gaiter thing this winter in the snow; I'm going to try GoreTex gaiters, though I'm not sure they offer any real advantages over plain coated-nylon gaiters - the only reason I got the GoreTex was because they were on clearance sale at the local outfitter.