Hi,
Well actually when I compile the code from the Github repository the anaglyph stereo c++ code does not seem to be used. After some confusion why my changes in the source (Manager.cpp) seemed to have no impact, I noticed that [gemwin] is no longer a native object as it is with the GEM shipped by Ubuntu. The source in Manager.cpp does not seem to be called at all, as it seems to be exchanged with a pd-native [gemwin] implementation. The abstraction [gemwin] however renders the anaglyph 3d erratically.
I have attached an image that demonstrates this problem. To me it looks like the green channel is opaque while above the red channel whereas the red channel is transparent when above the green one. The green channel should be blending with the red channel, but it blocks the red image information.
There is a pull request I have opened on Github with a fix for this problem (https://github.com/umlaeute/Gem/pull/187).
Best, Kilian