At the moment I’m working on some older project.
These were .all files from VST 5 era, I guess, converted these to .cpr using SL3.
But now I noticed, that in some of these projects the part colors dont change when changing track colors automatically.
Trying to find this project setting, but no luck yet… 
You must select the parts and choose “Default Color” for them to make them follow track color.
You used to be able to simply recolor Parts with the Color Tool…but Steinberg seems to have accidentally removed it from the Tool Palette in V6.5. See this:
I knew it would be a simple answer. 
I never select parts individualy and color them, just select the track and then select a color.
Guess with the old project I might have been messing around with coloring. 