So my forest and domain functional are Server 2003.
My main site has the RWDC’s and a remote site has a RODC.
For some odd reason, the GPO objects where not being APPENDED on the RODC when I made changes to the GPO objects on the RWDC.
The result was that the RODC was still applying GPO’s, but all the content of those GPO’s was outdated.
It looks like this is an issue that other people have faced (rarlely), and the solution is either to raise the functional level to Server 2008 to take advantage of the DFS replication of SYSVOL or to convert the RODC to a RWDC to allow proper writable replication to the SYSVOL on the RODC.