Sounds like your experiencing a compatibility issue between the 5.5 server and your 2003 version. In native mode Windows Server 2003 w/ Exchange 2003 will require full AD compatibility with other servers on the network to function fully i.e. replication tasks etc. In addition, there are many different technologies and changes to existing technologies between the two versions of Exchange which will prevent seamless interactions. The two versions (5.5 and 2003) can co-exist but expect there to be incompatabilities with certain functionality.