Run a fetch under webmaster tools to get your site re-indexed and checked once more for malware.
A couple of weeks ago we had Google Shopping reporting malware but webmaster tools reporting that everything was okay. Strange.
So we used this website: http://sucuri.net/ to identify the problem and now we have no issues. It's free to scan but they charge for a fix, however they provide enough information under the free scan to allow an eagle-eyed developer to pinpoint and neutralise the malware.
Hope this helps.