Clyde, maybe some of the files contain viruses. Eg. those files that has been uploaded by your members. I've encountered that 2 times, the only solution is delete that particular file. Scan your website here Kindly give us your url.
We still don't know what caused that but seems to be alright now.
Well, everyone can make mistakes, even Google On a more serious note - if your website is safe and it happens again, please let me know and provide some details from Google on what exactly they think is malicious.
I'm not active on the forum anymore. Please contact other forum staff.