You quoted from a source which stated the "sensitivity" of shipping manifests was not as much of an issue as the records maintained by foreign telecommunications companies which have U.S. customers. I quote the relevant section:
Foreign communications companies with American customers are commonly required to store business records in the United States. A senior U.S. official said the Bush administration considers shipping manifests less sensitive. The official spoke on condition of anonymity because of the confidential nature of the agreement."
You then questioned the intelligence of treating shipping manifests less securely:
Shipping manifests are said to be "less sensitive". Less sensitive than what? And if they have suddenly become "less sensitive," what's the point of the customs CIS program and the proposed CVSR program?
I took the opportunity therefore to explain to you what was meant by "sensitivity", why it is that telecomunications companies are routinely required to keep records IN THE U.S. for their U.S. customers, and why the administration was completely correct to assert that shipping manifests did not raise those same privacy concerns. The point being that "sensitivity" in this case applied NOT to security issues, but rather to PRIVACY issues.
The comparison of a shipping company to a telecommunications company was dubious at best for the opponents quoted in the article, but I wanted to stick to simply the explanation for the records retention differences.
I hope this has cleared up the confusion, and explains to you why the administration was correct on that particular point -- U.S. citizen telecommunications personal information is more "sensitive" than overseas shipping manifests.