Were the other boots you tried on too big? If so, that's probably why you didn't feel it.
I also only felt it on the left boot, but I think that's because my left foot is a tad bigger than my right so the boot was more snug. If you're right handed your left foot might be a little more muscular than your right, especially if you've played sports.
Either way, after wearing them about 6 times I didn't feel it any more. Since multiple people have commented on this same discomfort, I'm thinking that it's just part of the shoe that has to be broken in, not really a manufacturing flaw.