Keep in mind that if the site hasn't been crawled the code will return a blank set. It will also return a blank set if there is an issue on the site itself and you need to contact google.
A good test is to just create a test.html file and put the google code in it and upload it to your site and access it to ensure that it's not an issue with the google code in the first place (I've seen this happen with several client sites)