[Paint Bucket]

I do not believe I'm working another layer unless I made a layer unintentionally. Using the wand and going back and forth works; however, I was able to select the grid without using the wand before. 

[Paint Bucket]

I'm drawing a map and downloaded the gridcheckerboard plugin. After placing the grid I was able to fill the spaces of the grid with the bucket. On creating a second map, when I use the paint bucket, it fills the whole screen. I've toggled flood mode, moved tolerance from 0-100%, (including 1-20%), I toggled  antialiailising and clipping mode. I am not sure what I did to set up the paint bucket to fill the individual squares. Help would be appreciated.