Why is there a discrepancy between the number of links that Google webmaster tools (sitemap) says are pointing at a page and doing a Google Link: search. The webmaster tool documents 42 links but a Link search for the same page lists 0. What gives?
You can not trust the numbers in Google Webmaster Tools except to gauge how far Google has come in verifying which URLs from your XML sitemap it has indexed. Explained and also proven in this indexed urls article.
The Link: operator is generally only going to give a sample of the links. The webmaster tools will be more accurate, and more up-to-date. Personally, I wouldn't get too obsessed with this sort of thing. Concentrating on improving site content, site usability, relevant backlinks, terms of service compliance, etc, will give a better return than stats watching.