Thanks this was my problem as well, switching from using the softwareserial ports to the hardware 0/1 ports using the following code fixed my comms with the bee. In the stalker v3 it looks like you can switch from ports 0/1 to 6/7 by cutting a pad (see Seeeduino Stalker V3 | Seeed Studio Wiki).
// this is the pin on the micro that is connected to the tx pin on the bluetooth bee
#define BlueToothReceivePin 0
// this is the pin on the micro that is connected to the rx pin on the bluetooth bee
#define BlueToothTransmitPin 1
void setup()
{
Serial.begin(38400); //Set BluetoothBee baud rate to default value
delay(1000);
sendBlueToothCommand("\r\n+STWMOD=0\r\n");
sendBlueToothCommand("\r\n+INQ=1\r\n");
}
void sendBlueToothCommand(char command[])
{
Serial.print(command); // Use hardware serial port
delay(3000);
}