Wanted to alert people to an issue I came across with a client's hacked site. Apparently they were using an ad system (not sure which one caused it they had a few going) but the issues seemed to arise when the service switched to running Adsense ads.
The end result was the site being hit with the red warning screen about possible attack site for just over 48 hours.
Here is an article about the issue.
And My recent post about fixing it.
While this wasn't a WordPress issue, it is something to be aware of.
If anyone has recomendations for avoiding this or protecting files/directories from attacks like this, please let me know. All permissions were set and even had security scan plugin in place.