Yes this is normal. The PCIII is powered off the injectors and if you wit till the chekc engine light goes out, it will take a few more revolutions. From their site :
I am having trouble starting the engine when the Power Commander is installed.
Most Power Commanders are powered by the injectors on the bike. When you turn the key on, the fuel pump gets power and primes the fuel circuit. When this happens, the injectors get power, and the Power Commander also gets power and lights up. After a few moments, the fuel pump has pressurized the system, and usually shuts off. If the fuel pump shuts off, the injectors’ loose power, and the Power Commander shuts off. If you attempt to start the bike when the Power Commander is off, the bike may take longer to start than normal, until the fuel pump comes back on. The fuel pump may come on instantly, after a few engine revolutions, or on some bikes seemingly not at all. If the fuel pump does not come on, the bike will not start. We recommend starting the bike once you turn the key on. Do not wait for the fuel pump to shut off, or a check engine light to go out.
