I found this command line app for windows that does a pretty good job of multipart uploads. http://sprightlysoft.com/S3Upload/

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

if info["headers"].has_key("x-amz-meta-multipart-etag"):
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.