I had the same hackign attempt. it freaked me out and took a few hours to figure it out. I was uploading the new files to the IP directory but it was not overwriting ALL of them. In my case I had to delete the files from the directories THEN upload the new ones. I had even tried to force FileZilla to overwrite them but still the same thing.
Of course I backed up ALL the files before I deleted them. It's a no brainer to always back up everything before you do anything on the files.
Not sure if that is your problem,, but it was my problem and the reason I was getting the hacking attempt message. It had updated the sql database so it thought it was running new code but much of the code was still the old version.
You should try to do this.
let us now if it solved your problem.