The Button 64 has an "auto disconnect". When you start to upload a sketch to an Arduino the reset line is toggled. The B64 listens for this signal, when it senses it the B64 disconnects from the serial port and waits for the sketch to be finished uploading (the LED lights to show it is busy). The idea here is that you can leave the B64 on the Arduino and not have to remove it or flip a switch to upload new sketches.
Your issue sounds like you should look at the reset pin.