FE-4984 issue addressed the problem or broken handling of file and folder permissions on Windows OS. Windows OS is not Posix compliant system and has different file permission system. As Java lacks reliable way of managing Windows OS file permissions decision was made to stop managing that.
Instead the warning now is presented to the user intended to prompt the user to ensure that his FISHEYE_INST folder is properly secured and private keys are not accessible to unwanted users having access to the same machine. Apparently the warning message is confusing users.