Autotagger and multiple vocabularies

I was finally able to get Taxonomy Autotagger working but it only produces tags from one vocubulary.

I have multiple vocabularies that people can choose tags from but only the the tags on the first one listed on the content page will be used by autotagger even though both vocabularies are assigned to the correct Content type and they both have Multiple Select checked and the Tags and Required fields unchecked.

Is there a way to get autotagger to use both vocabularies or will I need a single vocabulary for all tags?