This may not be your issue, but if your boots are wet at all on the outside, try coating them with Nikwax or something to add some water repellency to keep the outers dry so they breathe better.
I only get blisters when the outside of my boot gets wet, even with a goretex boot. The goretex liner keeps the water from seeping in, but with a wet leather outer, the boot doesn't really breathe anymore since there is little to no gradient (difference in moisture content) from a damp foot to a saturated leather boot outer that is required for moisture transport to occur. Keeping the nikwak coating up has helped keep the outside of my boots dry, which in turn has cut down on pretty much all my blister issues. As will others suggestions about antiperspirants, sock changes, drying your boots, etc.