Kindly do a security scan of your site and did not see any issues at this time, however check your domain is currently on Google's blacklist, you can request that the warning be removed by visiting http://support.google.com/ webmasters/bin/answer.py?hl= en&answer=168328 and request a review. Once they see that your site is no longer harmful to users, they will remove the warning.
In the mean time, I would recommend that you change your FTP logins for the domain in question and do a anti-malware scan on your local machine used to service that site.
In the mean time, I would recommend that you change your FTP logins for the domain in question and do a anti-malware scan on your local machine used to service that site.