My Sony Alpha a58 and 68 have the same set up. I'm no techie so if this explanation is factually wrong in some places hopefully the techies will correct me.
You have a choice in manual mode of how and where you want to put the focus. You can choose center, wide, zone or flexible. Each one composes your shot differently in relation to where they pull in information about brightness.
Thank you Brian! I think that's what's happening. Really glad to understand this - it will make going forward in MF so much easier and with far fewer "what the heck" surprises.
And thanks for those helpful links too!
Here
are some good links to help you.