Andreas,
I am currently travelling, so can't check by myself.
i would not be surprised, if Nikon used the liberty of makernotes in the exif section of a file, to indicate which file is the primary copy of the image and which is the second copy. I.e. using code "00" for the first copy and "01" for the second copy - and all other things are identical.
Could someone please check with a camera with dual write mode, if the two files of this other camera have also one bit difference?
Doesn't explain the frozen status, but would provide some insights in the 993 photos with differences.
As said, just a guess - but easy to find out,
Andy