Can you attach the actual output style you are using as some of the special characters, like “link adjacent” don’t copy to the post. (if you have edited it or downloaded it, it will be in your my documents/library folder/Endnote/styles. If it was an installed output style it will be in the program folder/endnote/styles.)
So there are no cited pages? – the result is because if there are no cited pages, the comma followed by the period is a double punctuation and the period wins in that case. You can move the period to before the | at the end and it will only appear if there are cited pages, and the comma won’t disappear.
Are you sure you are using the new, edited output style in the manuscript? – because my test works. with both of the attached. Which ref type are you inserting. I tested with Journal.