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There can be many, many reasons for the chest pain.  I am not a doctor but I do know that you are correct in prolonged use of Naproxen can cause problems.  Another cause can be from the Methotrexate which causes many lung problems whos first symptoms can be chest pain.  Now with all that being said, you can also have rheumatoid arthritis in your chest bone, which I recently found out after a short stay in the hospital for chest pain.  In any case you should always call your doctor if you are having any sort of chest pain.  You also need to call your rheumatologist as soon as possible to see if he would like you to discontinue any medications or have some xrays done.  Chest pain is a scary symptoms that needs to be checked out in any case.  Good luck and best wishes!