On a default setup, when the setting $wgUseCombinedLoginLink is set to true, the links for logging in and creating an account are combined into one single link. When this is false, they are split into two separate links, as documented.

However, when $wgShowIPinHeader is also set to false, the create account link disappears, and only the "Log in" link is visible.

I noticed this on my main wiki, http://helpmebot.org.uk/wiki/Main_Page, so I set up a test wiki at http://prototype.helpmebot.org.uk/wiki/Main_Page with nothing special in the configuration except for three items:

$wgArticlePath="/wiki/$1";
$wgUseCombinedLoginLink=false;
$wgShowIPinHeader=false;

Version: 1.18.x
Severity: trivial
URL: http://prototype.helpmebot.org.uk/wiki/Main_Page