There is an old and serious problem with embedded templates that has not been fixed. Please have a look at this:
http://sourceforge.net/tracker/index.php?func=detail&aid=3158761&group_id=93107&atid=603138
Here I wrote a solution that worked for me in the given case, but it was not applied to Pywiki beacuse somebody showed an example where it causes another problem. It is not easy at all to catch embedded templates with regular expresses. Try my solution, but this is just an idea and not sure to work for you. You may want to adjust the regex to your needs (but don't forget you have changed it!).
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