There was an off-by-one error in the parsing command. This will be fixed in 7.0.0. As a workaround, just put out.pdf at the end, so run
qpdf --empty --pages *.pdf -- out.pdf instead of qpdf --empty out.pdf --pages *.pdf -- I always do it the second way, which is why I missed this. I didn't even have any test cases for it. Anyway, it's fixed now in master and will be in the next release. Sorry for taking sooo long to get to it. -- Jay Berkenbilt <q...@debian.org>