Even Ubuntu got a new version of this software... Reproducible: Always Steps to Reproduce:
fdupes 1.50-PR2 says my Ubuntu.
Also, the current version of fdupes has a bug which ignores large (> 2GB) files, which is said to be solved in fdupes_1.50-PR2, see http://www.mail-archive.com/debian-bugs-closed@lists.debian.org/msg170929.html
I don't use this software. Someone can promote faster adoption of this version bump by attaching a tested ebuild (even simply renaming it might be enough)
Added to CVS. Note that I dropped the md5sum-external USE flag because it currently conflicts with the new early matching support for large files.