I am not sure what is on either, since I saw a fansub of Perfect Blue several years ago at an anime meet. I believe most fansubs are not edited for content...so let me try to make a guess.
-There are model scenes where the main character is completely naked and contains no genitals but shows hair and may violate and R rating..not clear on that
-The rape scene is quite horrific, that may have been edited since I can't see how you could see her mental breakdown spiral without that scene
-Death by screwdriver from Pizza delivery 'mystery' person (can't spoil it for anyone) . I have seen ninja scroll, ressurection, wicked city and crying freeman. However, this scene..I could not watch. After the eyes being stabbed out...I had to cover my own eyes
If any of those scenes seem chopped up or are missing, that is probably what the difference is. Still, I am just guessing.