It is a simple tags issue although it would be nice if BA integrated better with WP's tagging system.
Under settings/simple tags/embedded tags there is this little warning
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Enabling this will allow Wordpress to look for embedded tags when saving and displaying posts. Such set of tags is marked [tags]like this, and this[/tags], and is added to the post when the post is saved, but does not display on the post.
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Why simple tags decided to do it this way I have no idea as I can not think of a single reason that you would want that feature.
I left embedded tags enabled. I added a footer in BA for some generic tags for each campaign. Like if I'm using an amateur feed I want the tag amateur. So the footer goes something like
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[tag]keyword1, keyword2[/tag]
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Then under manage/autotags/keyword list I added a fairly large collection of keywords.
It's not perfect but it does a pretty good job overall
I hope one of the improvements that happens in BA is that it automatically reads category/tag information in the feed and lets you decide whether to use it or not.