If you turn on the option SaveETagInMetadataForMultipart then the real md5sum for that part is written in the metadata under "x-amz-meta-multipart-etag"
So to make the two compatible, I changed line 636 in s3cmd
output(u" MD5 sum: %s" % info['headers'][''])
output(u" MD5 sum: %s" % info['headers']['etag'].strip('"'))
Seems to be working pretty well as part of my backup solution. After someone made a 12GB commit into SVN. Uggh.