Apparently over the past few days, one of the links on the website brought by a 3rd party was infiltrated and causing issues on some of the websites it appeared on (mine included). At the bottom of each blog entry there are three 'related links', and over the past 48 hours the company that provides that link was being attacked and hence any website that used that service was potentially exposed. Since those links are temporary and change each time someone comes to the site and reads that story, this is why when I scanned for malware I could not find it - it had already been eradicated.
They said they have since fixed it, but it might take 24-48 hrs before Google recognizes the website as safe again. Until then you might continue to get the message about this being a site potentially with security issues etc etc.
I've removed that linking service at the bottom of the posts for now.