I see this bug was closed, but perhaps it might be reopened? I seem to
have the same problem. I checked the files using the command line md5sum
tool, and the dupes have the same md5, but in the database there are two
different md5s for the dupes.

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Duplicate detection doesn't seem to be working for vertically aligned 
(portrait) photos
https://bugs.launchpad.net/bugs/439292
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