I had the same warning put on my site as well, over Xmas. It took 3 weeks to get it removed, and only when I took everything off the server and put it back on.  I did find a couple of older files that had some strange coding inserted in them, from Russia, that I did not put there. I located these files and removed them but it still took weeks to clear it up. Very upsetting and lost a lot of business while it was going on.  I think the files somehow got infected on my server, though the company would never admit it. I  have since switched my web hosting companies, as I could get no assistance from Globat whatsoever. I asked them to send the log files during that time so my tech rep could see what went on, and Globat sent me files before and after, but not those.  All in all it was a major hassle and I think Google is far too quick to slap that message on people's sites and far too slow to remove them.
Strange thing is, the warning message only appeared on the latest version of Firefox.
On Safari and older Firefox versions it didn't show up.
It is all cleared up but it made me very cautious of what I put on my server/site now.
Carol