1) All layers should match to presentation size. This is because stereoscopic modes don't duplicate layers to both eyes, but the 3D content inside layers. So layers which cover only part of the presentation size don't render correctly in top-bottom or left-right stereoscopic modes.
2) Because layer size issue and performance impact, presentations with subpresentations don't fully work in stereoscopic modes.
3) Currently effects are not supported in stereoscopic modes. So when switching from mono to any stereoscopic mode, effects are disabled.