Currently, shiny pokemon in boxes, in the party, and in trades do not appear shiny, even though shiny icons are available.
I know that the box glow is on the way, but shiny icons are a much more complete fix.
This is how the icons look, even though some should be shiny.
[img]http://puu.sh/2PMhw.png[/img]
However, these sprites should be used for pokemon when they are shiny.
[img]http://puu.sh/2PMlA.png[/img]
As, opposed to these sprites.
[img]http://puu.sh/2PMnd.png[/img]