In the official 2.4 release, the 2.5-dev snapshot, and upcoming 2.6 (as of commit 8ac0390b), the game does not run at all when a USB joystick is plugged in. When I run ./ufo, or double-click UFOAI.app, I see the splash screen but nothing else happens. top reports the CPU is pegged at 100% by the ufo process. The game does not proceed to the main menu, nor does the progress indicator move anywhere. I waited 5 minutes and still nothing happens.

In my custom compiled 2.6, I got this in the terminal:
$ ./ufo +set developer 1
---- endianness initialization -----
found little endian system

---- filesystem initialization -----
Adding game dir: /usr/local/games/ufo//base
Adding game dir: ./base
Added packfile ./base/0base.pk3 (15 files)
Added packfile ./base/0maps.pk3 (932 files)
Added packfile ./base/0materials.pk3 (54 files)
Added packfile ./base/0media.pk3 (19 files)
Added packfile ./base/0models.pk3 (2801 files)
Added packfile ./base/0music.pk3 (64 files)
Added packfile ./base/0pics.pk3 (1043 files)
Added packfile ./base/0shaders.pk3 (37 files)
Added packfile ./base/0snd.pk3 (362 files)
Added packfile ./base/0textures.pk3 (2721 files)
Added packfile ./base/0ufos.pk3 (138 files)
Could not load './base/0videos.pk3'
Adding game dir: /Users/tang/Documents/UFOAI-2.6-dev/base
using /Users/tang/Documents/UFOAI-2.6-dev/base for writing
executing filesystem.cfg
executing default.cfg
executing config.cfg

----- network initialization -------
libcurl/7.34.0 OpenSSL/1.0.1e zlib/1.2.5 libssh2/1.4.3 librtmp/2.3 initialized.

------ server initialization -------
mapcycle add: '+village2 mp2p_01' type 'fight1on1'
mapcycle add: 'training_a' type 'fight1on1'
mapcycle add: 'training_b' type 'fight1on1'
mapcycle add: '+oriental medium' type 'fight1on1'
mapcycle add: '+bridge mp' type 'fight1on1'
mapcycle add: '+africa small' type 'fight1on1'
mapcycle add: '+frozen small' type 'fight1on1'
mapcycle add: '+italy default' type 'fight1on1'
mapcycle add: 'farm' type 'fight1on1'
mapcycle add: 'estate' type 'fight1on1'
mapcycle add: '+japan default' type 'fight1on1'
mapcycle add: 'tower' type 'fight1on1'
added 12 maps to the mapcycle
...using mo files from /Users/tang/Downloads/ufoai/base/i18n/

----- console initialization -------
Console initialized.

------- video initialization -------
SDL version: 1.2.15
I: desktop depth: 32bpp
I: video memory: 0
I: video driver: Quartz
I: Available resolutions: 2560x1440 1920x1440 2048x1152 1600x1200 1600x900 1344x1008 1280x960 1344x756 1280x720 1024x768 1024x576 800x600 640x480 (13)
I: setting mode 0
I: disable multisample buffers
I: set swap control to 0
I: 2560x1440 (fullscreen: yes)
I: got 8 bits of stencil
I: got 24 bits of depth buffer
I: got double buffer
I: got 8 bits for red
I: got 8 bits for green
I: got 8 bits for blue
I: got 8 bits for alpha
I: got multisample disabled
I: got 0 multisample buffers
GL_VENDOR: NVIDIA Corporation
GL_RENDERER: NVIDIA GeForce GTX 775M OpenGL Engine
GL_VERSION: 2.1 NVIDIA-8.18.22 310.40.05f01
GL_EXTENSIONS: GL_ARB_color_buffer_float GL_ARB_depth_buffer_float GL_ARB_depth_clamp GL_ARB_depth_texture GL_ARB_draw_buffers GL_ARB_draw_elements_base_vertex GL_ARB_draw_instanced GL_ARB_fragment_program GL_ARB_fragment_program_shadow GL_ARB_fragment_shader GL_ARB_framebuffer_object GL_ARB_framebuffer_sRGB GL_ARB_half_float_pixel GL_ARB_half_float_vertex GL_ARB_imaging GL_ARB_instanced_arrays GL_ARB_multisample GL_ARB_multitexture GL_ARB_occlusion_query GL_ARB_pixel_buffer_object GL_ARB_point_parameters GL_ARB_point_sprite GL_ARB_provoking_vertex GL_ARB_seamless_cube_map GL_ARB_shader_objects GL_ARB_shader_texture_lod GL_ARB_shading_language_100 GL_ARB_shadow GL_ARB_sync GL_ARB_texture_border_clamp GL_ARB_texture_compression GL_ARB_texture_compression_rgtc 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_float 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_array_bgra GL_ARB_vertex_blend GL_ARB_vertex_buffer_object GL_ARB_vertex_program GL_ARB_vertex_shader GL_ARB_window_pos GL_EXT_abgr GL_EXT_bgra GL_EXT_bindable_uniform GL_EXT_blend_color GL_EXT_blend_equation_separate GL_EXT_blend_func_separate GL_EXT_blend_minmax GL_EXT_blend_subtract GL_EXT_clip_volume_hint GL_EXT_debug_label GL_EXT_debug_marker GL_EXT_depth_bounds_test GL_EXT_draw_buffers2 GL_EXT_draw_range_elements GL_EXT_fog_coord GL_EXT_framebuffer_blit GL_EXT_framebuffer_multisample GL_EXT_framebuffer_multisample_blit_scaled GL_EXT_framebuffer_object GL_EXT_framebuffer_sRGB GL_EXT_geometry_shader4 GL_EXT_gpu_program_parameters GL_EXT_gpu_shader4 GL_EXT_multi_draw_arrays GL_EXT_packed_depth_stencil GL_EXT_packed_float GL_EXT_provoking_vertex 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_texture_array GL_EXT_texture_compression_dxt1 GL_EXT_texture_compression_s3tc GL_EXT_texture_env_add GL_EXT_texture_filter_anisotropic GL_EXT_texture_integer GL_EXT_texture_lod_bias GL_EXT_texture_mirror_clamp GL_EXT_texture_rectangle GL_EXT_texture_shared_exponent GL_EXT_texture_sRGB GL_EXT_texture_sRGB_decode GL_EXT_timer_query GL_EXT_transform_feedback GL_EXT_vertex_array_bgra GL_APPLE_aux_depth_stencil GL_APPLE_client_storage GL_APPLE_element_array GL_APPLE_fence GL_APPLE_float_pixels GL_APPLE_flush_buffer_range GL_APPLE_flush_render GL_APPLE_object_purgeable GL_APPLE_packed_pixels GL_APPLE_pixel_buffer GL_APPLE_rgb_422 GL_APPLE_row_bytes GL_APPLE_specular_vector GL_APPLE_texture_range GL_APPLE_transform_hint GL_APPLE_vertex_array_object GL_APPLE_vertex_array_range GL_APPLE_vertex_point_size GL_APPLE_vertex_program_evaluators GL_APPLE_ycbcr_422 GL_ATI_separate_stencil GL_ATI_texture_env_combine3 GL_ATI_texture_float GL_ATI_texture_mirror_once GL_IBM_rasterpos_clip GL_NV_blend_square GL_NV_conditional_render GL_NV_depth_clamp GL_NV_fog_distance GL_NV_fragment_program_option GL_NV_fragment_program2 GL_NV_light_max_exponent GL_NV_multisample_filter_hint GL_NV_point_sprite GL_NV_texgen_reflection GL_NV_texture_barrier GL_NV_vertex_program2_option GL_NV_vertex_program3 GL_SGIS_generate_mipmap GL_SGIS_texture_edge_clamp GL_SGIS_texture_lod
OpenGL version detected: 2.1found GL_ARB_multitexture
found GL_ARB_texture_compression
found GL_ARB_texture_non_power_of_two
using GL_ARB_texture_non_power_of_two
found GL_EXT_texture_filter_anisotropic
found GL_EXT_texture_lod_bias
found GL_ARB_vertex_buffer_object
using GL_ARB_vertex_buffer_object
max vertex buffer size: 1048575
found GL_ARB_fragment_shader
found GL_ARB_shading_language_100
GLSL version guaranteed to be supported by OpenGL implementation postfixed by vender supplied info: 1.20
found GL_###_framebuffer_object
using GL_ARB_framebuffer_object
max draw buffers: 8
max render buffer size: 16384
max color attachments: 8
found GL_###_draw_buffers
using GL_ARB_draw_buffers
max supported vertex texture units: 16
max supported lights: 8
max texture units: 8
max texture coords: 8
max vertex attributes: 16
max varying floats: 124
max fragment uniform components: 2048
max vertex uniform components: 4096
max texture size: detected 16384
...but using 2048 as requested
Using low resolution globe textures as requested.
R_ProgramVariable: "TANGENTS" - No program bound.
R_ProgramVariable: "NEXT_FRAME_VERTS" - No program bound.
R_ProgramVariable: "NEXT_FRAME_NORMALS" - No program bound.
R_ProgramVariable: "NEXT_FRAME_TANGENTS" - No program bound.
R_LoadShader: Loading ./base/shaders/world_low_vs.glsl.
R_LoadShader: Loading ./base/shaders/world_low_fs.glsl.
R_LoadProgram: 'world_low' loaded.
R_LoadShader: Loading ./base/shaders/model_low_vs.glsl.
R_LoadShader: Loading ./base/shaders/model_low_fs.glsl.
R_LoadProgram: 'model_low' loaded.
R_LoadShader: Loading ./base/shaders/warp_vs.glsl.
R_LoadShader: Loading ./base/shaders/warp_fs.glsl.
R_LoadProgram: 'warp' loaded.
R_LoadShader: Loading ./base/shaders/geoscape_vs.glsl.
R_LoadShader: Loading ./base/shaders/geoscape_fs.glsl.
R_LoadProgram: 'geoscape' loaded.
R_LoadShader: Loading ./base/shaders/combine2_vs.glsl.
R_LoadShader: Loading ./base/shaders/combine2_fs.glsl.
R_LoadProgram: 'combine2' loaded.
R_LoadShader: Loading ./base/shaders/convolve3_vs.glsl.
R_LoadShader: Loading ./base/shaders/convolve3_fs.glsl.
R_LoadProgram: 'convolve3' loaded.
R_LoadShader: Loading ./base/shaders/atmosphere_vs.glsl.
R_LoadShader: Loading ./base/shaders/atmosphere_fs.glsl.
R_LoadProgram: 'atmosphere' loaded.
R_LoadShader: Loading ./base/shaders/simple_glow_vs.glsl.
R_LoadShader: Loading ./base/shaders/simple_glow_fs.glsl.
R_LoadProgram: 'simple_glow' loaded.
SDL_ttf version 2.0.11 - we need at least 2.0.7

------- sound initialization -------
SDL_mixer version: 1.2.12
... requested audio rate: 44100
... driver: 'coreaudio'
... audio rate: 44100
... audio channels: 2
... loaded ogg vorbis support
CL_SetClientState: Set new state to 1 (old was: 0)

------- input initialization -------
Calling SDL_Init(SDL_INIT_JOYSTICK)...
SDL_Init(SDL_INIT_JOYSTICK) passed.
1 possible joysticks
Killed: 9

If instead I run without +set developer 1, the tail end of console messages is:

------- input initialization -------
1 possible joysticks
joystick 0 opened - set cvar in_joystickNo to change this
Killed: 9