It sounds like that layer is solid white, which at 40% opacity will make the slate appear a medium gray.
Check the thumbnail for that layer in the layer list.
If it is a white square, make it the active layer and delete it's contents (Delete key).
It should change to the grey checkerboard of a fully transparent layer.
Then redo the highlight grid.

Other things to check:
Does that layer have an alpha channel. (It needs one.)
Is the grid width still 1.