The problem was with shader-based pipeline with disabled "advanced effects" in options.
In this case we don't use RTTs and gl_FragCoord contains values in range of whole window. So fo 2 players we still get gl_FragCoord.y = 0..window_size instead of gl_FragCoord.y = 0..window_size/2.
The easiest way to solve it seems to be modulo it by current viewport size. It should be compatible with advanced pipeline as well as single-player games.
Atm. I'm not sure if this should be applied to 0.9.2 branch. It should work fine, but needs some testing.
