I copy the files while spamd is running and restart it after the copy.
I run also sa-learn --sync in the slave server.
Do you run sa-learn --sync on the master?
I ask because I wan under the impression that this just synchronized the journal with the database. As you have copied everything across to the slave from the master, it should be in an identical state, until you run the sync, at which stage the DBs are slightly out of sync. I am not sure but suspect that the problem may lie in this area.
mike