What do you mean that you started it without a key? Is the large stove knob key not in the ignition? Do you have at least one fob?
If you don't have a fob and you just walked up to the bike and pressed the stove knob key in to start the bike, that means that the fob is somewhere ON the bike. You cannot start the bike without a fob being near the bike somewhere.
The red flashing LED is normal, it's the immobilizer. The LED will flash for ~24 hours after the bike has been shut down. It's still working after the LED stops flashing though.