Ok here is my issue. I have a template that that has cfinclude files for the
menues and repeating region code blocks. These included files also have cfset
variables in them to determine the current page and set the active menu.

When I do simple text changes everything works fine when the files is
republished. However if i add or delete a repeated region and republish the
file the included files are not longer dynamically included it seems as though
contribute actually download the contents of the included file and instead of
reinserting the code for the cfinsert file it actually publishes the html code
that was in the included file and drops any server site stuff I am using
contribute cs3