I was going to try and transfer a map from my lcd screen and noticed that when I turn on the ignition the pwr commander led's scanned up and down and then went off along with the lcd screen.
Does that normally happen or should it stay on?

That is normal on Power commander. You can only communicate with it when the engine is running. If you want to talk to it without the engine running then use a 9v PP3 battery on the supplied lead and plug this into the power commander.
Not sure how the LCD screen thingy works though.

Cheers for that!
I needed to be sure that a "faulty" power commander wasn't the cause of my failed starting problem.
Still looks like flooded plugs!