When initiating a replica set using rs.initiate(), the resulting rs.conf() object has the local hostname in it. When changing it to the fully qualified domain name using this method:

conf = rs.conf()
conf.members[0].host = "fully.qualified.domain.com:27017"
rs.reconfigure(conf)

the resulting rs.conf() object is updated with the new domain name. Alas, rs.status() reports the old hostname.
After a server restart, the rs.status() command reports the right values.

This problem affects, for example, connecting java clients to the server which need the FQDN to function. These read the slave/master information from the replica status object, and pay no attention to rs.conf().