If you've updated the table plus add-on post upgrade, have you tried rerunning the wiki markup migration tool?
If that doesn't work, and you can actually copy out the wiki markup of the tables, what happens if you then (in edit mode) click Insert > wiki markup and paste the table contents into the wiki markup box. When you click insert it should convert the markup on the fly. Then you should have your table in xhtml format in the text editor.
Hope this helps!
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