I realize this thread is rather old (2013), but I'm currently experiencing a blacklisting issue with my website, JMAPC.com. Both Google and McAffee Threat Intelligence feel it's a risk.
Please excuse my somewhat terse question. I find the web-based editor on this site maddening ... moving on ....
My website (jmapc.com) had been hacked about two months ago. We cleaned up the site. However, we still found ourselves on several blacklists (Google, McAfee, Fortiguard). This state persisted for two months, with no idea why we were still on the list.
This issue is somewhat moot, since yesterday I requested a review from McAfee, Fortiguard and Google. All three sites have since removed me from the blacklist. Life is good!
Obfuscated code is frequently found in malware so yes that may be the reason.
However the site was hacked and subsequently blacklisted so there's no way of telling.
The algorithms for keeping a site blacklisted after a cleanup allow for an extended period before a rating gets changed.
(I regret that at the moment personal circumstances do not allow me to undertake investigations in depth - back in 2013 I had more time to do this sort of thing. So any conclusions about the blacklisting of your site are tentative. Still, at least the site ratings got reset, which is good).