Duplicate cookies due to iRule

I don't think you're explicitly removing the existing cookie before adding a new one. One sort of quirky thing about HTTP cookies is that a unique instance is defined not just by the cookie name, but also a combination of its value, path, expires, and other attributes. So,

Set-Cookie foo=test1;path=/;secure;httponly
Set-Cookie foo=test2;path=/;secure;httponly
Set-Cookie foo=test2;path=/;httponly

Are all separate cookies as far as the browser is concerned. Inserting a cookie with the same name, by virtue of a different "signature", is actually creating a new cookie.

I also typically don't like to set the HttpOnly flag using the HTTP::cookie command because it can behave badly. Instead here's what I would use to replace a given set of cookies and set the secure and HttpOnly flags:

when HTTP_RESPONSE {
    foreach aCookie [HTTP::cookie names] {
         if the cookie does not already have an HttpOnly attribute

        if { ( [HTTP::cookie httponly $aCookie] equals "disable" ) or ( [HTTP::cookie secure $aCookie] equals "disable" ) } {

             get cookie value and path
            set value [HTTP::cookie value $aCookie]
            set path [HTTP::cookie path $aCookie]

             get and insert domain if it exists
            if { [HTTP::cookie domain $aCookie] ne "" } { set domain "domain=[HTTP::cookie domain $aCookie];" } else { set domain "" }

             get and insert expires only if it exists
            if { [HTTP::cookie expires $aCookie] ne "" } {
                set expires_local [clock format [expr [clock seconds] + [HTTP::cookie expires $aCookie]] -format "%a, %d-%b-%Y %H:%M:%S GMT" -gmt true]
                set expires "expires=$expires_local;"
            } else {
                set expires ""
            }

             remove the original cookie
            HTTP::cookie remove $aCookie

             insert a new cookie via HTTP header inject
            HTTP::header insert "Set-Cookie" "$aCookie=$value;path=$path;${domain}${expires}secure;HttpOnly;"
        }       
    }
}