This issue appears to be due to a limitation with C4D recognizing the way we break kits into logical parts.
Previously we broke apart our kits by materials so each object would only have 1 material. With our 4.0 update, we are now breaking the kit into "logical parts" which requires us to combine and apply multiple materials to each new part. Our understanding is that C4D does not easily recognize that and will duplicate the material several times.
To resolve this issue, our C4D Ambassador recommends a tool called C4D Tag Cleaner. Simply click "Clean Materials" and it cleans up your entire scene and removes all of the extra materials on the objects.
How to Clean up the Extra Material Tags in Cinema4D
These tools are designed to quickly clean scene objects from empty selection tags and materials assigned to empty selections (assigned to nothing).
STEP 1: Download the zip file. http://www.rendereverything.com/ktools-for-c4d/
STEP 2: Open C4D, go to Edit→ Preferences. At the bottom of the Preferences, there is a button that reads “Open Preferences Folder”. Click it and it’ll open a new window.
STEP 3: Inside of the preferences folder is a folder called “plugins”. Open it. Unzip the KTools directly into this folder. Make sure it is inside its own folder called “KTools”.
STEP 4: Restart Cinema4D.
STEP 5: Once open, go to Extensions→ KTools. Select “Clean Materials”. The tool will clean the entire scene and remove all of the materials not used on each object.
The scene should now work as intended.
We sincerely apologize for the inconvenience. We are working to fix this problem as soon as possible.