Does anyone know why there would be a blue flag above my base with a blue light circling my base?

This is a new feature of the game that allows an R4 or R5 of your alliance to set 'pins' on the world map for your entire alliance to see.

Perhaps your leadership was just playing around with you or they actually have a reason that I wouldn't be able to answer without talking to the player who placed it. The person placing the pin has the ability to add text to it, so see if it says anything.

If you are playing DD, I've seen it being used to get people's attention when your opponent forfeits and people keep attacking buildings after being asked to stop.