I'm reluctant to repeat my episode mentioned before to confirm the facts, but as I recall that when it came to the 'fix', I only had one entry in the 'Group or user names' on the Permissions for Software - that was Everyone.
Also on Advanced Security Settings for Software there was either no entry, or just the one: Everyone - Full Control.
Finally I think the 'Inherit from parent ...' checkbox was unchecked, while the 'Replace permission entries ...' checkbox was checked.
You could try again with these settings - but as I said before I'm no expert and can only say what worked for me.