When EndNote starts to add in-text citations as {Author, year #nr} instead of the format you expected, it is probably because "Instant Formatting is Off." Look in the right column of the Word document tab Bibliography. There you can choose between Instant Formatting is Off or Instant Formatting is on. If it is Off, change to On and try again!
You can also choose to allow the #nrs temporarily, and when you have finished writing, click on “Update Citations and Bibliography”. This will immediately format all your citations into your selected output style.
