This can happen if the role map dictionary maps artifacts to roles that are still in the reading order. What is the role map? It is one of many "dictionaries" in Acrobat that allow Acrobat to create documents that can be read across many different platforms. Basically, dictionaries are columns of tags or attributes, the attribute on the left is "mapped" to the attribute on the right. Recently, I was assessing a pdf (I'm a web Accessibility Consultant) in which the following appeared:
/artifact /P
This means that, as it stands, every time you make something an artifact, it will be treated as plain text, and still be in the reading order.
How do you find the role map? Right-click on the tag that you want to artifact, and choose "Edit Role Map". This will bring up the role map dictionary. I am quite sure that you will find that /artifact has been mapped to something that will keep it in the reading order.