Autometa is great—been using it without issue for many WordPress versions.
However, since upgrading to 2.9, it does something that it’s not meant to. Normally, when one enters one’s own keywords, Autometa will not generate any.
Now, it deletes the self-generated ones and its automatic generation comes into play—in my case twice, so there are two keywords’ fields.
It’s probably a very small thing that needs to be changed—I hope you can look into it, as I rely a great deal on unique keywords for SEO.