I've just switched over to using sbuild (from pbuilder) to build my packages for upload to Debian and I've run into this same bug.
My workflow generally involves building the source package by whatever means is necessary for the package (depends on team, vcs, etc). Then I run adt-run, sbuild (possibly with --run-piuparts), and do a bunch of other testing on the package before I upload it. One of the last things I do is explicitly run lintian over the changes file. Because pbuilder copies the orig.tar.gz even for -2+ packages, lintian is usually happy, but when building the package with sbuild, lintian will thrown an internal error before you even get to the good stuff. I can manually cp the orig.tar.gz from the tarballs directory to the results directory after sbuild completes and then lintian is happy, but I wish I didn't have to do this one extra step.
