I'm getting 404 errors with JetPack.
Jetpack stats are referring to a bad location for the files. in my case - it SHOULD be:
sitename/wordpress/wp-admin/admin.php?page=stats&blog=30737063&day=2012-01-22
But instead - is now trying to link to:
sitename/wp-admin/admin.php?page=stats&blog=30737063&day=2012-01-22
and in some cases is trying to refer to another directory that does not exist as being in a 'mystats' directory, and even eliminating the /wordpress/ directory for the code:
sitename/my-stats/?blog=30737063&day=2012-01-22
Note that it is eliminating the "/wordpress/ directory from it's links.
Dunno what happened to change it - but with the widespread errors, I don't believe it to be our sites.. I believe it's somewhere on JetPack's side.