There may be some differences due to exiftool version when you diff the 2 files, but I know of no problems with version 7.30 that could cause this.
Could you send me the two images so I can take a look? My email is phil at owl.phy.queensu.ca Thanks.
Re^5: XMP, Image::ExifTool, strawberryperl
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Just to close this out. The problem was not exiftool. After writing the meta information, the image was resized with imagemagick causing the problem. Turns out that imagemagick was adding an extra space after the XMP identifier at the start of the APP1 segment, which would cause most XMP readers to ignore the segment. However, exiftool recognizes non-standard XMP segments, so it can still read the information.