I recently had a similar problem with my package libgpiv2; the differences between upstram .tar.gz and .orig.tar.gz., I think , is due to the differences in the root direcory names. Programs/scripts like dh_make create a new directory 'name.orig' if you start to debianize an upstream package from scratch. During building the package the name.orig is packed into name.orig.tar.gz. The md5check sum's of the CONTENTS of upstream and progname-version.orig were identic, but the md5check sum's of tar.gz and orig.tar.gz FILES were different.
The only remedy against this is to rename the name.tar.gz (from upstream) to name.orig.tar.gz before you start building the package. Maybe there should be filed a bug against dh_make for this? Gerber -- Main developer of G[ov c.s.; software for Particle Image Velocimetry http://gpiv.sourceforge.net public key: D39A2B64
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