Yes, I think I've worked out what's going on here. Correct me if I'm wrong, but I believe that you are getting the 'double pulse' when you move the spotlight off the lowest enemy and onto another with no gap between them. So, if the two enemies had the same Y coordinate they would overlap (See below):
This is caused by your 'Else' function which disables the Pulse effect. The Else function only triggers when the condition: "Enemy is overlapping Spotlight_Detect" is false, but because there is no gap in between the two, it never triggers. Therefore, the first is still pulsing because it was never told to stop, and the second is pulsing because it is correctly the lowest now. In fact, the first is no longer even in the loop because it's no longer in the spotlight. That means we have to deal with it in another block. This can be a little tricky so let me take some time to think about it.