In most cases if there is a problem in IE6 it is because of a bad path to the IE6 conditional css. Since conditional CSS is placed in a comment, the location is not updated by Dreamweaver when a page is placed in a subdirectory or comes from a template.
In this case you need to update:
"../CSSMenuWriter/
to:
"../../CSSMenuWriter/
anywhere it occurs (specificaly for the ie6 conditional code where it is wrong).