On my Linux hosts I'm running rkhunter. On a newly configured host it lately reported the following warning:

Warning: The SSH and rkhunter configuration options should be the same:
        SSH configuration option 'PermitRootLogin': no
	Rkhunter configuration option 'ALLOW_SSH_ROOT_USER': no

On first sight the warning does not seem to make much sense, as both configuration options seem to be set to the same value (no).
But digging further reveals that they are stored slightly different:

# file /etc/rkhunter.conf
/etc/rkhunter.conf: ASCII text
# file /etc/ssh/sshd_config
/etc/ssh/sshd_config: ASCII text, with CRLF line terminators

Turns out that rkhunter is also checking the line terminators as part of the configuration values, and warns because they are different.

Knowing this, the fix is simple: run dos2unix on the CRLF file