Im having the same problems.
I had to replace every js file, and now, it now, it only appears when I try to access to the admin panel (/wp-admin/).
When I use Sucuri, it says "WordPress version outdated: Upgrade required", but I have 3.3.1 version. I have tryied re-installing it, but I was unlucky. Any help?
I think is a problem relates to the theme. I don't why, but I think the theme was also infected.
Updated: I managed to solve "WordPress version outdated: Upgrade required" problem, I just uploaded again my theme. However, It still appears the malware warning when I try to enter to the admin panel.
Besides, if I try to add a new post, my antivirus (Eset Nod32) detects a trojan: Agent.Nef Trojan.
What is happening?