It seems that treatment can mess things up in some wierd and wonderful ways! My periods have certainly been affected, cycle messed up and lots of spotting before and after my period and yes much more painful than they used to be. I also had lots of intermittent bleeding especially after sex, I put up with it and waited until my 6 month check and some of it turned out to be due to a huge ectropian as a result of treatment. If things dont improve I would say go see your gp, sometimes scaring can make it difficult for things to flow out properly causing more pain than usual.
I am currently having my first period after a cone biopsy and period paind are horrific so I know how you feel.