SCCM 2012 secondary site not publishing to Active Directory

So I recently made a secondary site for SCCM 2012. I didn't set the permissions on the site management container in AD until after the secondary site was already created. Afterwards, I set the secondary site computer account to have full control on the systems container and everything below it, but the entries still haven't been created in AD. The main site's entries are there, and the permissions look indentical for the two computer objects. Did I screw this up by not setting the permissions until after the secondary server was created? Any ideas how to troubleshoot? Here's the entries in the sitecomp.log.

Publish Servers in Active Directory. SMS_SITE_COMPONENT_MANAGER 3/15/2013 1:09:59 PM 2252 (0x08CC)
  Processing forest mydomain.com. SMS_SITE_COMPONENT_MANAGER 3/15/2013 1:09:59 PM 2252 (0x08CC)
   No publishing account defined for this forest, will use the machine account instead. SMS_SITE_COMPONENT_MANAGER 3/15/2013 1:09:59 PM 2252 (0x08CC)
    DS Root:DC=mydomain,DC=com SMS_SITE_COMPONENT_MANAGER 3/15/2013 1:09:59 PM 2252 (0x08CC)
    Searching for the System Management Container. SMS_SITE_COMPONENT_MANAGER 3/15/2013 1:09:59 PM 2252 (0x08CC)
    LDAP://CN=System Management,CN=System,DC=mydomain,DC=com container exists. SMS_SITE_COMPONENT_MANAGER 3/15/2013 1:09:59 PM 2252 (0x08CC)
   No Fallback Status Point installed on the Site SMS_SITE_COMPONENT_MANAGER 3/15/2013 1:09:59 PM 2252 (0x08CC)
   Size of Signing Certificate: 0 SMS_SITE_COMPONENT_MANAGER 3/15/2013 1:09:59 PM 2252 (0x08CC)
   Signing Certificate: SMS_SITE_COMPONENT_MANAGER 3/15/2013 1:09:59 PM 2252 (0x08CC)
 Failed to get top level site code SMS_SITE_COMPONENT_MANAGER 3/15/2013 1:09:59 PM 2252 (0x08CC)
  Not able to get [MIF Collection] settings. SMS_SITE_COMPONENT_MANAGER 3/15/2013 1:09:59 PM 2252 (0x08CC)
 Failed to get top level site code SMS_SITE_COMPONENT_MANAGER 3/15/2013 1:09:59 PM 2252 (0x08CC)
   Current copy of the Site Control File is invalid. Not able to read SMS_SITE_COMPONENT_MANAGER section of sitecontrol file of top level site. SMS_SITE_COMPONENT_MANAGER 3/15/2013 1:09:59 PM 2252 (0x08CC)
 Waiting for changes to the "D:\SCCM\inboxes\sitectrl.box" or "D:\SCCM\inboxes\sitecomp.box" directories,