See http://www.google.com/url?sa=t&source=web&cd=1&ved=0CBwQFjAA&url=http%3A%2F%2Fgroups.google.com%2Fgroup%2Fmongodb-user%2Fbrowse_thread%2Fthread%2F3a831d2675b0ec12&rct=j&q=google%20groups%20copydatabase%20failed&ei=mltBTvzrF4Hq0gHO-Om2CQ&usg=AFQjCNEAdHW-X8VFfuZ52talNbQ6GIyp7g&cad=rja

Copying is incomplete or does not happen at all.

Workaround is to script something like:

var mongoTo = mongod; var mongoFrom = mongos;
var collections = mongoFrom.getDB( "test" ).getCollectionNames()
var dbTo = "test2"; var dbFrom = "test"
var collections = mongoFrom.getDB( dbFrom ).getCollectionNames()
for( var i = 0; i < collections.length; i++ ){
var cursor = mongoFrom.getCollection( dbFrom + "." + collections[i] ).find()
while( cursor.hasNext() )

{ mongoTo.getCollection( dbTo + "." + collections[i] ).insert( cursor.next() ) }

}