Sometimes your computer will require you to install two USB devices when you first plug in the Tuneboy cable. If you only installed one, that could be the problem. However, If you have already obtained the ECU# then your USB settings should be correct, as you would have been unable to retrieve the ECU# without the proper settings. I would double check that you have entered the password correctly, and that the tune you are attempting to load is in fact for your engine year/model. Also, make sure the red light on the USB plug is flashing red. If it is not, then you don't have communication between the bike and the computer.
Here is Tuneboy's serial port instructions:
"By default the Serial Port (communications port) is set to COM1. Ensure that the selected port is the port that you are using to connect the cable to the bike. Change this if necessary.
If you have a TuneBoy USB cable that shows up in the serial port list as "USB Serial Port (COMnn)" then you should set the cable type to USB.
If the cable shows up as "TuneBoy Cable(COMnn)" then the cable type should be set to 2.
Serial port 2 is only used when you use the Dynojet Tuning Link software."