To make a long story, short:
We were hacked through our FTP server by brute force and the jerkface re-wrote some of the files to include a hidden iframe that linked back to a malicious site. So we weren't the host of the malware, but a link back to it...
Anywho, we reset everything back to square one and took measures to ensure it doesn't happen again. Google still has us listed due to the issue coming to the forefront last night, and we have already submitted the request to recheck it since it is all clear. So yes, expect Chrome to still say "WARNING" until we finally clear their waivers.