Stacks not working correctly?

I use Stacks in da place for my Application and Download folder I keep in my dock, anyways, the stack icon I use for Application works fine, but every time I download something into my downloads folder, the stack icon disappears and gets pushed back by the new thing I've downloaded. Even when I open Downloads and choose to put the icon first, it still doesn't work but my application one works fine.

I don't understand.