All projects are visible to users under Dashboard Config - Add Project, when their permissions are set at project level to allow access only to a single project.
This does not allow access to the issues within other projects but does allow users to see what projects are stored within Jira.
I've recently resolve a bug that sounds similar to yours.
I refer to
JRA-1484.Please confirm whether yours is the same bug. If so its been fixed
Thanks,
dave