My assumption was that we set the configuration and then call connect on iOS, this is how it is being used in PERealTimeComunicationManager.m - 
- (void)startReceivingMessages {
    if (![PubNub sharedInstance].isConnected) {
        [PubNub setDelegate:self];
        [PubNub setConfiguration:self.pubNubConfiguration];
        [PubNub setClientIdentifier:[Utility pgid]];
        [PubNub connect];
    }
}
I think need to set the client identifier before doing connect (or initializing the pubnub on Android side)