Hi
Welcome to the MedHelp forum!
If there is no pain on passing stools, it is unlikely that the pain is due to fissures. There is a chance that you have developed abdominal adhesions due to previous surgeries (if there is a history of these). Other causes of rectal pain are hemorrhoids, tight anal sphincter (can be caused by adhesions too) and Levator anis syndrome or spasm of levator ani muscles. Less common causes are cancer, infection, IBS and foreign body in rectum.
I think you should discuss these possibilities with your doctor. It is difficult to comment beyond this without examining. A comprehensive investigation is required keeping all the points in mind. Take care!
http://www.merck.com/mmhe/sec22/ch249/ch249a.html
The link above is what first came to mind when I read your message. It is a link describing "pelvic floor disorders." Whatever the cause, if it keeps you awake at night and causes pain, it is best to see your doctor. Better safe than sorry.