Hosting accounts are usually not that accurate in telling when or how the websites are infected with viruses or Trojans. The best way would be frequently scanning your hard drives because the way most sites and pages are attacked is nowadays not because of online threats but the viruses attacking FTP tools. I once experienced the problem because all of the HTML files I was uploading were having some iFrames problems caused by a Trojan and the Google alert is because of that. Try scanning your disks with an updated AV program and then reupload the files. In some cases getting in touch with Google after saving the accurate files types would help returning things back to normal.
Also turn off FTP. Use SSH instead its much more secure. then install AVG on your server.. its free http://free.avg.com/us-en/download.prd-alf