I had my first fissure as a 17 year old in 2001.
It started as mild pain generally after going. Was kind of a burning, itching feeling.
I visited the doc he said I had a fissure and to put anusol on the fissure to prevent the the itching. The medicine worked well and eventually the fissure went away.
Fast forward to 2009. Another fissure popped up. This time it was much more painful while going, and there was visible blood on the stool and on the paper itself. I went to the doc again, he told me to visit a color rectal specialist. I went to the specialist he used an anuscope on me and said I had a fissure. Never mentioned any other problems, even at one point said my prostate looks great. Prescribed me Nifidene/Lidocaine compound and to take 2 stool softners a day, drink plenty of water, vegetables fruit etc. Took maybe a month or so, and eventually it went away.
Now to 2012. Noticed the pain reering its ugly head again the day after thanksgiving. Again a fissure. But this time I noticed that unlike before I was having more pain after I went and I had a hard time sitting. Was kind of a gnawing, tearing, type ache, and usually would throb. Went to the CS again. Said I reopened the fissure and didn't see any signs of anything else, this time he only examined me via his own eyes rather than the anuscope. So I deal with the fissure change my diet and take the Colace again. The Colace seems to have little effect, or sometimes it will have an effect. Anyhow, the fissure seemed to go away around XMAS and I was pain free for about a week. I could barely feel the fissure. I kept taking the Colace just to be safed and stuck to my healthy diet. On New Years some friends came over, I had one piece of pizza and about 15 small blue cheese and apricot spread with flour and butter baked into these bite sized snacks.
Well the next day the fissure said HEYYY IM STILL HERE!! DID YOU MISS ME? a little bit of blood on the stool and on the paper itself.
So there is my story. I noticed that I usually have two BMS in the morning. One right when I wake up and am thinking about it. Then another an hour or so later. Then for the rest of the day or at least 4 hours after I will have the pain of what I think is a spasm where it hurts at the fissure site and sometimes a bit inside my anus, these are the worse. It seems like the BMS themselves are not too painful a bit, but not as bad as the annoying pain afterwards that last.
Has anyone else dealt with this? I take the baths when I can and use the compound nifidpene and lidocaine? Assuming my fissure is chronic because I have had it for nearly 6 weeks. I have a follow up with the CS soon. What should I expect another exam? More medicine?
Sorry for the long note.

Hi..In response to your comments below...
"I noticed that I usually have two BMS in the morning. One right when I wake up and am thinking about it. Then another an hour or so later. Then for the rest of the day or at least 4 hours after I will have the pain of what I think is a spasm where it hurts at the fissure site and sometimes a bit inside my anus, these are the worse. It seems like the BMS themselves are not too painful a bit, but not as bad as the annoying pain afterwards that last."
...I am almost exactly the same as you are describing. A couple or 3 BM in the morning that are now (and only now...) not too bad, but after the BM, I get the same pain that you describe.
My CRS told me to eat whatever the hell I want!
I take a daily dose of metamucil as well as a stool softener before bed. Things are getting better but I think you have to be very dedicated to the soft stools...
otherwise tears will recur.
Hopefully time will heal all.
Good Luck.
Bajan