stcrim - What do you mean by "had to roll the site back"? Also, how long ago was this?
Without further information, this database problem does seem to be the most likely cause. Sometimes, after a glitch like this, it takes Google a while to sort things out.
Also, have you checked that it is in fact a penalty? Have you completely disappeared from the index, or just for competitive searches? Have you tried searching with the dupe filter disabled?
Take a look at the Hot Topics [webmasterworld.com] section, pinned to the top of the Google Search forum home page, and look at the "Penalties, Sandbox, and Trust" section. In particular, I'd start with this post....
Am I penalized? What type of penalty do I have?