It's music to
my ears.
It strikes me as potentially a question of style or tone. Given the "quiet reserve" it might help to curb outward enthusiasm. I, and people I know, often tell people to have a great day but in such a low-key way that it doesn't register as strange. I've seen other people (with Southern accents) do the same thing in a manner which is natural to them, but strikes New Englanders as out of the ordinary and, given experience, fake, even though I don't doubt you mean it sincerely.
This can be a tough place to "break in" (particularly if you can't easily "pass" as local) and people can be gruff, but when you're in you're in. While I try to be courteous to everyone, and never affirmatively rude, I think many people here view "the human element" not as unimportant, but as something primarily applicable to one's immediate circle. With some people, like in a store, the contact will be so brief there's not much you can do to get past the gruffness or even rudeness. The question is whether you can shrug that off and think it's worth it here. It's easy for me since I'm used to it and like everything up here so much there's no doubt it's worth it.
People here are busy, live in a fast-paced culture, and the winter has a bad effect on morale and mood for many. There are a lot of people crammed into a small area with Byzantine roads and a spotty public transit system. It doesn't always lead to observance of niceties. Some (many) try to be courteous (I do) while others don't do as well in that department. You either take the bad with the good or move on. It's unfortunately unlikely that the negative aspects of the place will change, only your reaction can.
I have been made to wait for an hour in a restaurant in the south, and had other less than pleasant experiences, because I didn't have the slightest hint of a southern accent. There is some degree of regional hostility that has not yet been eliminated. I know people in the Boston area who, though it's not particularly fair, have come to cringe at a southern accent because of the perception that that is the region that gave us 8 years of Bush. I do think the 2000 and 2004 elections hardened regional antipathy to some degree, and that may improve as time passes.