Normally password protection will affect every subfolder and file below it. I am not too sure whether there is any way to stop this though.
All your e-mail accounts will be protected by default with the username and password that you supply when they are set up so there is no need for you to manually password protect the accounts. This would just add a second layer of unnecessary password protection as well as causing yourself the other problems that you are encountering.
Hope that helps
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