Hello, again! It appears that there are various other projects using the same md5.c code from Colin Plumb, and some of them have made changes relating to non-32-bit platforms. See, for instance, http://cvsweb.xfree86.org/cvsweb/cvs/lib/md5.c.diff?r1=1.1.1.1&r2=1.1.1.2 as an example of one project's changes.
I have incorporated the minimal set of those changes, which were released to the public domain, and the result is that my amd64 Debian box runs the program correctly. By 'runs the program correctly' I mean both that the false positives go away and that the program produces the same md5 checksums as the 'md5sum' program does. A patch is attached to this message. I hope you find my patch helpful and timely for inclusion in etch. Thanks! Ari Johnson
sxid-64bit-clean.patch
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