Okay, I am now working with a copy of the problem epub. This epub passes epubcheck. In all ways it just looks normal.
I then made a Checkpoint of the epub in order to look for any changes.
I then fired up ePubTidy and the plugin gui started up just fine.
I used the same setting as in the picture posted above and ran it and got nothing to indicate that anything was done.
I then checked the procecess span tags, and hit Process Text again and a list of 3 span tags immediately appeared.
So the plugin is running and at least properly handling span tags.
I will now try to add some debug print output to epubtidy to see what is going on.
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