I also encountered this issue today.
Here is the configuration that caused the problem:
- Create a flexible content field with field name “page_modules” in field group A
- Create a field group B
- Add a clone field and use “page_modules” as the field name (NOTE: this is the issue – using the same field name in both places)
- In the “Fields”, select the “Page Modules” field (and only that field, not “All fields in group A”)
- Leave the clone field set to “Seamless (replaces this field with selected fields)”
With this configuration, the fields show up correctly on pages with field group B, but the flexible content layouts are not saved.
Workaround: Simply rename the clone to something like “modules” or “cloned_modules”. Then it works 🙂
