This is one of those computing terms which have an annoying clash. Directory could be an element in a list of file directories, or a directory of users. These are two very different things.
The user folders which you have changed the permissions of are file directories, and not what the error is about. The error is trying (badly) to tell you that it cannot write to the user directories that are configured (the internal one by default)
I would stop the service, wait for a few seconds to check it has fully shut down, move the log files from <jira home>/logs/ to somewhere safe (this is me being a bit lazy - if you start with empty logs, you won't spend ages looking through older entries for the problem). Then start Jira again, and visit the url, churning through until the error happens again, which won't take long. Then stop it again.
The logs should now contain an error message telling you why the user directories can't be read.
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