It has been brought to my attention that there are some blank areas of the new maps, notably in Jefferson County, KY. I researched the problem and both to my consternation and delight, it is due to errors in the Tiger/Line data and not the program I wrote to resolve out the new ZCTA's.
The 2005SE Tiger/Line data for state 21, county 111 (Jefferson County, KY) has ZCTA's only for the bordering counties but none at all for the ZCTA's internal to the county. I guess somewhere along the line this information was lost. I can only hope that it will be added back in at some point.
In the event that other missing data is suspected, it can be confirmed by using the 2000 ZCTA vs. 2005SE ZCTA tool (http://maps.huge.info/newzips.htm) I wrote. Please report any problems of this nature to me using the contact form (click here).