Same issue here!
Saving checkboxes inside of a group is not working properly. Outside of it works correctly.
Reproducable Steps:
0. Create CPT
1. Create Fieldgroup
2. Create a Group field
3. Create a Checkbox field with some options inside the Group
4. Create a Post within the CPT
5. Check some options of the Checkbox field in the post editor
6. Save and reload the page
This will result into having no checked indication in any of them.
It will be correctly queryable though. It seems to be registered in the database but there is no visual feedback in the post editor.
