Password Protecting a Zip File/Folder

I have a large ammount of sensitive data that is on a shared drive at work.
The select associates that need access to the files have the password, an I
am trying to password protect a zip file version of the folders.
Currently I only have skelton folders, no data stored in them, while I set
up protection. The files are not empty, but they have no Word/Excel/PDF files
in them. I have gotten the password prompt to come up when I open some
folders that are 'password protected'. Other files have a password assigned
but I still have access to them without entering the password.

My question is why does the password pick up sometimes and not others? I
have set up the password protection the exact same way in every case.