Issue was caused by Cycles using render options from rendering scene, not from active scene. For now solved by passing render resolution inside RenderEngine structure. This probably could be solved in more general way, like adding bindings for RenderEngine->Render, which would avoid passing options like is_animation, came_override and so via RenderEngine. Would think about this a bit more and probably would do that. The same issue happens in trunk as well, but not consider such a change trunk-ready, would want to make more tests and probably clean the code a little bit before commiting this into trunk.