Note the first cube, which is not contained within the difference, completely disappears.
My build info is:
OpenSCAD Version: 2014.03
Compiler, build date: GCC "4.7.2", Mar 9 2014
Boost version: 1_53
Eigen version: 3.1.1
CGAL version, kernels: 4.0.2, Cartesian<Gmpq>, Extended_cartesian<Gmpq>, Epeck
OpenCSG version: OpenCSG 1.3.2
Qt version: 4.8.2
MingW build: No
GLib version: 2.38.2
OPENSCADPATH: <not set>
OpenSCAD library path:
/home/chris/.local/share/OpenSCAD/libraries
/usr/local/lib/openscad/../../share/openscad/libraries
GLEW version: 1.9.0
OpenGL Version: 1.4 (2.1.2 NVIDIA 304.116)
GL Renderer: GeForce 9400M/integrated/SSE2
GL Vendor: NVIDIA Corporation
RGBA(8880), depth(24), stencil(8)
GL_ARB_framebuffer_object: yes
GL_EXT_framebuffer_object: yes
GL_EXT_packed_depth_stencil: yes
Using QGLWidget
GL Extensions:
GL_ARB_depth_texture
GL_ARB_draw_buffers
GL_ARB_fragment_program
GL_ARB_fragment_program_shadow
GL_ARB_framebuffer_object
GL_ARB_imaging
GL_ARB_multisample
GL_ARB_multitexture
GL_ARB_occlusion_query
GL_ARB_point_parameters
GL_ARB_point_sprite
GL_ARB_shadow
GL_ARB_texture_border_clamp
GL_ARB_texture_compression
GL_ARB_texture_cube_map
GL_ARB_texture_env_add
GL_ARB_texture_env_combine
GL_ARB_texture_env_crossbar
GL_ARB_texture_env_dot3
GL_ARB_texture_mirrored_repeat
GL_ARB_texture_non_power_of_two
GL_ARB_texture_rectangle
GL_ARB_texture_rg
GL_ARB_transpose_matrix
GL_ARB_vertex_program
GL_ARB_window_pos
GL_ATI_draw_buffers
GL_ATI_texture_float
GL_ATI_texture_mirror_once
GL_EXT_abgr
GL_EXT_bgra
GL_EXT_blend_color
GL_EXT_blend_equation_separate
GL_EXT_blend_func_separate
GL_EXT_blend_minmax
GL_EXT_blend_subtract
GL_EXT_draw_range_elements
GL_EXT_fog_coord
GL_EXT_framebuffer_blit
GL_EXT_framebuffer_multisample
GL_EXT_framebuffer_object
GL_EXT_framebuffer_sRGB
GL_EXT_multi_draw_arrays
GL_EXT_packed_depth_stencil
GL_EXT_packed_pixels
GL_EXT_point_parameters
GL_EXT_rescale_normal
GL_EXT_secondary_color
GL_EXT_separate_specular_color
GL_EXT_shadow_funcs
GL_EXT_stencil_two_side
GL_EXT_stencil_wrap
GL_EXT_texture3D
GL_EXT_texture_compression_dxt1
GL_EXT_texture_compression_s3tc
GL_EXT_texture_edge_clamp
GL_EXT_texture_env_add
GL_EXT_texture_env_combine
GL_EXT_texture_env_dot3
GL_EXT_texture_filter_anisotropic
GL_EXT_texture_lod
GL_EXT_texture_lod_bias
GL_EXT_texture_mirror_clamp
GL_EXT_texture_object
GL_EXT_texture_rectangle
GL_EXT_vertex_array
GL_IBM_rasterpos_clip
GL_IBM_texture_mirrored_repeat
GL_INGR_blend_func_separate
GL_NV_blend_square
GL_NV_copy_depth_to_color
GL_NV_depth_clamp
GL_NV_fog_distance
GL_NV_fragment_program
GL_NV_fragment_program2
GL_NV_fragment_program_option
GL_NV_light_max_exponent
GL_NV_multisample_filter_hint
GL_NV_packed_depth_stencil
GL_NV_point_sprite
GL_NV_texgen_reflection
GL_NV_texture_compression_vtc
GL_NV_texture_env_combine4
GL_NV_texture_rectangle
GL_NV_vertex_program
GL_NV_vertex_program1_1
GL_NV_vertex_program2
GL_NV_vertex_program2_option
GL_NV_vertex_program3
GL_OES_compressed_paletted_texture
GL_OES_read_format
GL_SGIS_generate_mipmap
GL_SGIS_texture_border_clamp
GL_SGIS_texture_edge_clamp
GL_SGIS_texture_lod
GL_SGIX_depth_texture
GL_SGIX_shadow
GL_SUN_multi_draw_arrays
GL_SUN_slice_accum