You should be calling pbuilder as usually for the first upload to your
archive (will include source) and with --binary-arch for all subsequent
uploads.

It might be interesting to see why the .diff.gz is modified; it could
either be a difference in the output on i386 and on amd64, or it could
be a timestamp in the gz stream.

-- 
Pbuilder gives a different md5sum for a source .diff.gz archive in result than 
the one it started with
https://bugs.launchpad.net/bugs/118180
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