Miami has deep ties to the Caribbean. So when a devastating earthquake struck Haiti on January 12, The Miami Herald mobilized for one of its biggest stories of the year. Reporters were on a flight to the Dominican Republic that night and filing from Haiti the next day. The sense of mission extended to the paper’s Web site, where a special Haiti channel pulled together print coverage as well as video pieces, photo archives, and Twitter feeds from correspondents. Multimedia editor Rick Hirsch thought his site could open a window onto the tragedy for audiences around the world. “Haiti really is a local story for us,” he explains.

According to the Herald’s server logs, his hunch was right: traffic leapt by more than a third in January, to 35 million page views, the only time it broke 30 million in the six months before or after. Nearly 5.9 million different people visited the site that month, another high-water mark for the year.

But not according to comScore, the media measurement firm that, along with rival Nielsen, purports to be the objective word on what Americans do online. ComScore recorded fewer than 9 million page views for the Herald, and barely 1.6 million “unique visitors.” Even more distressing, comScore—whose clients include major advertisers and ad agencies—had the paper’s page views actually declining by 40 percent the month of the earthquake. “Those trends just don’t make sense,” insists Hirsch, whose newspaper subscribes to comScore as well. “We know our traffic went through the roof.”

The open secret of online publishing is that such wild discrepancies are routine. Whether you ask The Washington Post or a stand-alone site like Talking Points Memo (TPM), you’ll hear the same refrain: publishers looking at their own server data (via software like Omniture or Google Analytics) always see much more traffic than is reported by Nielsen and comScore, both of which extrapolate a site’s audience by tracking a small “panel” of Web users, just as Nielsen does for its famous TV ratings.

“The panel-based numbers are atrocious,” says Kourosh Karimkhany, TPM’s chief operating officer, pointing out that Nielsen and comScore have a hard time measuring workplace Web surfing. “But as long as they’re equally inaccurate for our competitors, it’s okay. It’s something we live with.”

For that matter, the two ratings firms frequently disagree with each other. In May, for example, Gannett’s various properties commanded 37.5 million unique visitors according to comScore, but only 25.6 million according to Nielsen. ComScore gave Washingtonpost.com an audience of 17 million people that month, but Nielsen recorded fewer than 10 million. And so on.

It’s fair to ask how business gets done amid such uncertainty. Who should a site’s sponsors—or for that matter, its journalists—believe?

Publishers say the cacophony scares away advertisers, a conclusion supported by a 2009 McKinsey & Company study commissioned by the Internet Advertising Bureau. Executives from Newser and MLB.com told The Wall Street Journal’s “Numbers Guy” columnist last February that undercounting by Nielsen and comScore keeps them off the radar of major advertisers, and hurts their bottom lines.

This messy situation has yielded any number of white papers and task forces; reform efforts are currently under way at the IAB, the Media Ratings Council, and the Newspaper Association of America, among others. Last year CBS, NBC, and Disney led the formation of a “Coalition for Innovative Media Measurement,” that seeks to establish a cross-platform standard to gauge total media usage.

In response, comScore has unveiled a new “hybrid” approach that claims to mash up panel results with server-side data for a more accurate count. This is a little ironic, since the raison d’être for the user panels is that server data can’t be trusted because it counts computers, not people, who may visit a site from more than one machine. Whatever the technical merits, one comparison found the “hybrid” counts boost audiences by 30 percent on average; some sites, like The Onion, saw traffic nearly triple. Nielsen has a similar system in the works.

Lucas Graves is an assistant professor in the school of journalism and mass communication at the University of Wisconsin. Follow him on Twitter at @gravesmatter.