Very strange. Is it intermittent? Did you check the XMP sidecar and time stamp?
I looked up a file I changed yesterday - and the .xmp sidecar is showing an OLD timestamp!
Best I can see, this is only happening for files that were originally edited by an older version of Camera Raw (perhaps CS4 or CS5).
Do you have your camera-raw set to record changes in the XMP sidecars or in the central CR database? Maybe the settings can be different between the versions of Photoshop and this is confusing things.
I looked in Photoshop CS6 Edit / Preferences / Camera Raw...
The first setting "General / Save image settings in:" is set to "Sidecar .xmp files".
I also tried renaming the .xmp file and editing the .NEF file again. No new .xmp file created. Looks like CR is using its internal DB despite the preferences.
Something is not right here...
Resetting preferences may work, but I have spent much too much time getting all preferences just right for my workflow. I would hate to lose all that.
This is a specific problem with ACR (7.2) not able to overwrite a previous .xmp file. If I delete the existing .xmp and make changes to the .NEF file, a new .xmp IS written out.