make sure that the user that you've use to delete the folder has the state permission to delete the files.
check the state permission on the workflow that you've currently working if the user that you use has a folder add/delete.
check all the state in the workflow and also in the folder permission
can you attach a print screen with the workflow and folder permission,
so that i can see if you've set the folder and state permission correctly.
just try first check the folder and state permission of the user..
You may also need to check the "ignore permissions from previous states". If the files had been in a state without delete, you need to move them into a state with delete and the ignore flag checked, Just adding the ability to delete to their current state may not be sufficient. I had to send files through a transition into a new state to delete.