I have automatic color loops but not flashing lights. I had the same problems you’re facing when I used a custom DTH. I’d used one for the scene capability, but realized I lost the CoRE customization.
I uninstalled the custom and now using a slightly modified standard DTH that you can find here:
For scenes, I also use CoRE. It’s a bit more work to recreate them, but it’s a good tradeoff for CoRE capabilities.
Good luck!