Having a similar issue, but it does seem to be more than just a change in brightness, but also some significant change in colour (perhaps the one leads to the other, to the human eye). My tv is a samsung PN51F5500 and I'm using a Sony BDP-S5200. Like the above person, I've checked for all those little features that I'd assume could do something like this, eco- sort of things, but nothing's changed.
Out of curiosity, what film were you watching? I don't remember this with The Lego Movie, but I feel like, for some reason beyond me, the changing of aspect ratio on the Guardians of the Galaxy bluray is effecting these shifts. Sometimes it seems like the picture is fine in 16:9, without the black bars and more prone to this flicker when in 21:9, where black bars are present on top/bottom.