DUH!
I just looked at the config file for the millionth time and finally saw what the problem was. I didn't set the comment config to require login before comments. Everything was set to zero. I just put a 1 on 'commentsloginrequired' and it's doing what it's supposed to do.
// +---------------------------------------------------------------------------+
// | MISCELLANEOUS SETTINGS |
// | |
// | These are other various Geeklog settings. The defaults should work OK |
// | for most situations. |
// +---------------------------------------------------------------------------+
// this lets you select which functions are available for registered users only
$_CONF['loginrequired'] = 0; // all of them, if set to 1 will override all else
$_CONF['submitloginrequired'] = 1;
$_CONF['commentsloginrequired'] = 1;
$_CONF['statsloginrequired'] = 0;
$_CONF['searchloginrequired'] = 0;
$_CONF['profileloginrequired'] = 0;
$_CONF['emailuserloginrequired'] = 1;
$_CONF['emailstoryloginrequired'] = 0;
$_CONF['directoryloginrequired'] = 0;