Hi David,
"Not all Materials work properly" – opens a wide variety of ideas about what could go wrong. One point could be that the Shaders don't rely on UV(W) data, and the UV Tag has overlapping polygons, etc. With little to go on, please have a look here:
https://www.youtube.com/watch?v=TvZiDsODf8k
I assume the product is not currently for public use, but let me try it anyway to find out.
The Manual states that images and UV(W) projections are allowed. I would say that sRGB is the best bet for the colorspace.
Materials based on Shaders or Layers will not work, especially Nodes. This brings up another question: You did not mention whether you have set up the project in Standard or Redshift 3D render space. Each would lead to a different bake option.
For Redshift, the process is different
https://help.maxon.net/r3d/cinema/en-us/Default.htm#html/Baking.html
Materials and glTF
https://help.maxon.net/c4d/2024/en-us/Default.htm#html/FGLTFEXPORTER-GLTFEXPORTER_GRP_MATERIALS.html?TocPath=Configuration%257CPreferences%257CImport%252FExport%257CglTF%257CglTF%2520Export%2520Settings%257C_____4
In summary, start with a proper UV mesh for the object and use only textures to produce surface results.
How to create UV? This is also a question that relates to your object, but have a look here:
https://cineversity.maxon.net/en/results?term=UV+Workflows
The less specific a question is, the more questions I typically have in return. I'm so sorry about the torrent of links and such.
If you have question, please let me know.
All the best