File Permissions borked after "Repair File Permissions"
Permissions repair only affects folders and packages installed by apple and during software updates and it leaves most user folders alone. 

You should be able to run it again to fix anything not correct. If there are still issues, you likely have a user definition corruption issue and might have to attack that head on. Which specific app it folder has these issues? Edit your question and this can also be edited once more detail is provided.