Larry et al.-
 
I definitely go with the dog/multiple use/post classic scenarios.  A
few years back, I wrote a "note" for Historical Archaeology describing
a shallow, rectangular pit located under a mid-19c house in
Mecklenburg County, VA.  I think the original use of the pit was for
hearth fill because the pit was very close to and centered on the
chimney foundation, but the later use seems to me to be dog "bed."
Both corners of the pit closest to the chimney had been elongated
diagonally toward the corners of the house.  The elongation suggests
that perhaps something was crawling into and out of the pit on a
fairly regular basis (no, not an archaeologist; I was only in there
twice).  One of the elongated "dog ears" runs off toward the corner of
the chimney foundation to the door to the crawl space; the other leads
of toward the other side of the chimney, toward the underside of an
old porch.  Both areas may have provided some access for animals.  I
note also that the house was used first as the Nelson Harper Crowder
family home, then was occupied by one of the bachelor heirs, and
continued to be used perhaps into the 1980's as a hunting "camp."
There are also tobacco sticks in the attic of one addition, so the
place continued to be frequented by humans and animals for a variety
of purposes.  So, although I never found (never looked for) bones
under or around the house,  there is certainly a lot of activity,
human and otherwise, which could have brought domestic and wild bone
to the site at a time when smell and cleanliness would have been a
fairly minor issue.