Make sure you are deleting folder on righthand side
Step 1: Click on My folders
Step 2. Click on Folder you want to remove located in righthand pane
Step 3. Click Delete (Make sure Folder is empty of all contents first)
Step 4: Verify that Check for newer version of stored pages is set to Automatically
Step 5: Verify you are not trying to delete a shared file.
Step 6: If trying to delete a folder, verify that all files are deleted within that folder or any subfolders