It works perfectly fine in both modes here. I'll need more output than "it does not work" to know what's wrong. What's your hardware, what drivers are you using (did you enable compositing?), has it ever worked before or is it the first time you've tried? What is the output when running 'cairo-dock -o --log debug' in a terminal (please don't post here, it is very long), also did you look on their bug tracker for a similar bug?

http://lmgtfy.com/?q=cairo-dock+opengl+invisible+icons

Apparently intel chips are known to have issues, try 'cairo-dock -o -i' or simply use cairo mode for the time being.

I have an Intel HD 4000 mobile graphics Card on a Lenovo Thinkpad Edge S430 with SNA enabled. I just installed it the first time and it shows invisible icons. Only the icon I hover with the mouse are shown. -o -i does not work. glx disabled (-c) works

cairo-dock -o --log debug (the most important output)
(...)
debug : (/build/src/cairo-dock-3.2.0/src/gldit/cairo-dock-opengl.c:cairo_dock_initialize_opengl_backend:191)
got 4 FBConfig(s)
warning : (/build/src/cairo-dock-3.2.0/src/gldit/cairo-dock-opengl.c:cairo_dock_initialize_opengl_backend:202)
couldn't find an appropriate visual, trying to get one without Stencil buffer
(it may cause some little deterioration in the rendering) ...
debug : (/build/src/cairo-dock-3.2.0/src/gldit/cairo-dock-opengl.c:cairo_dock_initialize_opengl_backend:208)
this time got 10 FBConfig(s)
message : (/build/src/cairo-dock-3.2.0/src/gldit/cairo-dock-opengl.c:_get_visual_from_fbconfigs:149)
Strike, found a GLX visual with alpha-support !

============================================================================
Cairo-Dock version : 3.2.0
Compiled date : Mar 28 2013 19:42:53
Built with GTK : 3.6
Running with OpenGL: 1
============================================================================(...
(...)
message : (/build/src/cairo-dock-3.2.0/src/gldit/cairo-dock-opengl.c:_post_initialize_opengl_backend:121)
OpenGL config summary :
- bNonPowerOfTwoAvailable : 1
- bFboAvailable : 1
- direct rendering : 1
- bTextureFromPixmapAvailable : 1
- bAccumBufferAvailable : 0
- Anisotroy filtering level max : 16,0
- OpenGL version: 3.0 Mesa 9.1.1
- OpenGL vendor: Intel Open Source Technology Center
- OpenGL renderer: Mesa DRI Intel(R) Ivybridge Mobile


message : (/build/src/cairo-dock-3.2.0/src/gldit/cairo-dock-backends-manager.c:cairo_dock_set_renderer:254)
cairo_dock_set_renderer (efe770:(null))
message : (/build/src/cairo-dock-3.2.0/src/gldit/cairo-dock-manager.c:gldi_load_managers:191)
gldi_load_managers()
(...)

Thx for the info, there are already several bug reports about this, here's one: https://bugs.freedesktop.org/show_bug.cgi?id=55036, unfortunately there's not much I can do about it. I'll close this task, please use cairo mode and follow the upstream development.