Comment 44 for bug 408065

"couldn't find an appropriate visual ourself, trying something else, this may not work with some drivers ..."

means it didn't find an FBConfig that fits its needs (4 channel, depth=32, if I remember corerctly)
so then it's trying to find a visual from another way, but usually it won't give better result (it will probably give a visual with no transparency, hence the black background.)

I don't have the code in front of me, but it's in cairo_dock_get_opengl_config(), in cairo-dock-draw-opengl.c, ~ line 1650