Is there any possibility that it is iframe related? That the iframe itself is generating tags, because it is a 'page'(html) in its own right, and then the index.php generates the tags also?
If perhaps this is the case, how can we test the situation to create a solution?
A note on the side: Unfortunately, as I am not the full time guardian of most websites that I create, I have to hand them over to their respective owners, the process for them has to be as automated as possibly, and therefore it is not really possible for me to ask them each time they create a new page that is particularly raising this issue to go into their MySQL and delete the doubled up tags.
I will be less available for testing and resolving over the next four weeks due to business meetings, but will do all I can to help