When you use FQDN do you mean the full hostname of the DC which is the correct term or do you mean the Active Directory domain name (ie. yourdomain.local)?
If you specify yourdomain.local\sysvol, it will go to the first one that answers. There is no PDC in 2003+ domains. All DCs replicate and can apply updates.
If there are files or policies missing from the second DC, you may want to run NETDIAG and DCDIAG to determine why.