I am also experiencing this problem.
About a year ago, it surfaced and there was some discussion, and fixes offered. Review this WordPress trac ticket #4248, and the links at the bottom of: http://trac.wordpress.org/ticket/4248.
Text of that ticket:
I'm not sure if this is even appropriate here, since it's not really WordPress' fault, but there's a bug in PHP 5.2.2 that prevents XMLRPC from working properly. Basically, $HTTP_RAW_POST_DATA is never set, even when called via POST or with the config option set to always be on.
It's possible to work around it in WP 2.2 by adding one line to the beginning of WordPress' xmlrpc.php file, right before the first mention of the variable.
$HTTP_RAW_POST_DATA = file_get_contents("php://input");
It's apparently fixed in the PHP CVS, but who knows how long it'll be before 5.2.3 comes out.
Anyway, I don't know if you'll want to include a workaround for a single-version bug (though this is the most current "stable" release) or what impact this would have running on other versions of PHP, but I thought I'd post it just to convey the info.
The links below this WordPress trac ticket explain much of the detail of the problem, tracing it to a bug in PHP.
But this is over a year later - Oct/Nov 2008, and I am experiencing this problem - wordpress.com stats shows in admin as a bar graph labeled 'Region A' and 'Region B' and years on the x-axis 2003-2005.
I am using:
PHP version 5.2.6
Apache version 2.2.10 (Unix)
MySql version 5.0.51a-community
FireFox 3.0.3 on Mac OS X 10.5.5
I turned off caching (WP super cache).
I altered XMLRPC.php as specified above in the Comment thread of "Automattic Stats, or PHP 5.2.2 vs WordPress XMLRPC".
I did change permalinks from my custom to one of the offered configs, saved those changes, then changed back to my custom settings, as suggested in this Comment thread (to 'flush' something or other).
None of that fixes the problem. And I have not come across any analysis of the problem less than a year old. Maybe something in PHP 5.2.6 breaks something that had been fixed in versions after 5.2.2? Anyway, "IT's BACK."
Very annoying, and interesting, problem now resurfacing a year and a half later in Oct/Nov 2008. Sincerely hope someone out there who has some information about this problem, what is causing it now, and how to work around it.
Thanks in advance,