Filling Selected Area on a Layer Problem

Hello

I am working with Photoshop CS6.
Since a few days I have the problem to fill a selected area properly.
For example I have a square on Layer 1.
I then create Layer 2 above Layer 1.
While I am on Layer 2 I select an area which overlaps the square on Layer 1 and I try to fill it.
But it doesn't work properly and only fills the part which doesn't overlap the square on Layer 1.

I am definitely on Layer 2.

Is there something I might have changed in the settings?

Here is screenshot of the problem:

Thanks!