2.63 rc1 from blender.org (as well as other older versions from graphicall)
open default scene --> save a new .blend ---> ctrl + s to see the confirm dialog ---> make a change -> go FILE > Save
now make another change --> Ctrl +s and it saves auto with no confirm.
This is different behavior to previous versions of blender. Not really a show stopper or anything, just a bit unnerving.
If anything, it is that first confirmation that probably should not show. If you have a file saved (i.e., assigned it a name), you make a change then hit "Save" expected behavior in almost all file-based applications is to simply save. The only time you should get the confirmation you mention is if you have chosen to overwrite an existing file whose path/name does not match the one currently loaded in the UI. Going to go back through docs around this feature to better understand the expected behavior.