Hi Johann,
For group, the value of a group is always an array. If it's cloneable, then the value is always array of arrays (2 level depth array), even when it's empty. So, for group, you should check the subvalue as well, not just empty
on the group value.
For other fields, I can't replicate the bug. There is also 1 open pull request for similar bug on Github (for oembed field), but I can't make the same bug:
https://github.com/rilwis/meta-box/pull/703
Do you see the same problem? Can you post your code?