Officially, there is no such thing as a zip code boundary, a zip code area or any geographic representation of a zip code. To the USPS, a zip code is a delivery route, not an area. Here's a good explanation from the Census bureau comparing the ZCTA to the USPS Zip Code.
The difference between the 2000 census ZCTA and the 2005SE based ZCTA's is the age of the data. The 2005SE ZCTA's are dated as of December (or there abouts) 2003 and the 2000 census ZCTA's are sometime before 2000, probably 1998.