what year is your scoot? 07's did have fuel pump issues.

 

I was told by the dealer to let the "check engine" light go out before starting. not sure why but they said it so I do it. I would suspect you have either a fp problem or as stated some type of sensor for the efi. I had the same type issue years ago on a car I owned and it turned out to be the crank sensor. It my case I pulled it out and it had some corrosion on the pickup I cleaned it off and never had an issue again. I suggest checking codes and go from there.

 

The dealer gave you good advice:

The bike's ICM/ECM is a computer. Much like your computer at home needs to "boot-up" when you turn it on. The ICM/ECM "computer" on the bike needs time to initialize and gather readings from the bikes various sensors.