Often, the first time you know about malware hosted on your website, it's already banned by Google. Finding out why it's been banned is sometimes tricky.
Sites hosting malware can be infected directly through a vulnerability in the site's software or as we're finding, it's external links and advertising to infected sites that cause issues, particularly if the advertising uses an IFRAME to 'inject' content into your site.
If you get reports that your site is hosting malware, there are a number of tools to help you identify the cause and remove the malware.
A free service is the excellent 'Unmask Parasites' at http://www.unmaskparasites.com/
It's also worth reading the comprehensive guide to dealing with Google Malware Warnings at http://www.unmaskparasites.com/malware-warning-guide/
Of course, contact our support department as soon as possible to prevent further issues and to get your site back online and we can advise further action to prevent your site being a malware target in future.