Graphical problems such as corrupted textures, missing effects, clipping light sources, burn-in or transparent objects being opaque can usually be solved by switching to the software renderer by pressing F9 while the game is running or via GSdx's config panel. If using the Direct3D 11 renderer, try the OpenGL renderer, as it may be more accurate. If you're using a stable build, try switching to the most recent nightly or dev build. Newer development builds of the emulator may have fixes or other features added to the hardware renderers, which remove common glitches like red or green bars appearing on the screen.