John,
A couple of thoughts:
First, BBF is the invention of the devil when it comes to birds walking or jumping limb to limb. I lead photo workshops in Africa and invariably, there is a beginner (I'm not talking of you) that has read about BBF from Art Morris and feels it is magic. Unfortunately, they forget to refocus once the animal or bird moves. When the subject is as close as your example, a simple tilt of body angle is all it takes to put the body out of focus. In your first two images, the focus point is clearly behind the bird, so this could have been your issue.
Second, the birds look VERY CLOSE. It looks like the bird may have been inside your minimum focus range setting. Another very common mistake.
I know the bird looks bigger in frame on the last two vs the first two with 7D MkII. Was it the exact same lens with exact same settings?
Also regarding MFA, this doesn't change focus point inches, it changes it small mm amounts. This is not the issue.
On shots where no focus point was active, was this a middle shot from a burst? I've often had this happen and had sharp birds in flight as the bird stayed on the same plane as the prior shot which did have an active focus point.