Thanks, this worked, but I had to rearrange the options. so that RegEx
was excluded before the include

FileSet {
        Name = "StandardWindowsFileSet"
        Include {
                Options {
                    exclude = yes
                        RegEx = ".*\.lnk"
            }
        Options {
                        signature = MD5
                        compression=GZIP
                        WildDir  = "C:/Documents and Settings/*/My Documents"
                Wild     = "C:/Documents and Settings/*/My Documents/*"
                RegExDir = "C:/Documents and Settings/[^/]+$"
        }
        Options {
                        exclude = yes
            Wild = "C:/Documents and Settings/*"
            }
                File = "C:/Documents and Settings"
       }
}

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