The difference seems to be precisely 2. (Graph = downloads + 2). However, this does not occur on all packages (e.g., the latest release of HTML_Progress does not display this discrepancy)

Looking at a bunch of download statistics for different packages, there's some huge discrepencies.

Here for example:
http://pear.php.net/package-stats.php?pid=338

Total downloads: 550, June downloads: 750.

This probably has to do with the package_stats and downloads tables being out of synch.  Below is a script that can get them in line.  Martin will have the various permissions needed to run it, so I'm foisting this off onto him.

<?php

require_once 'DB.php';
$db =& DB::connect('mysql://pear:pear@localhost/pear');
$db->setFetchMode(DB_FETCHMODE_ASSOC);

$db->query('lock tables downloads write, package_stats write');

$res =& $db->query('select release, count(*) as quant
from downloads group by release');

while ($res->fetchInto($row)) {
    echo implode(' ', $row) . "<br />\n";
    $db->query('update package_stats set dl_number = '
               . $row['quant']
               . ' where rid = ' . $row['release']);
}

$db->query('unlock tables');

?>

The database has been updated.