Hi Warren -
Data from 2000-2004 were technically from a pilot of the ACS. Full implementation did not really begin until 2005.
Also, one of the other main changes in the survey was the inclusion of group quarters into the sample, starting in 2006. This, theoretically, should not affect household populations (e.g. grandparents caring for grandchildren are in households, not GQ) BUT it may affect the population controlling that occurs for small area estimates.
There may be other issues, but those are the two that come to mind.