Dear Eric,
we made the same observation using qiime cutadapt dumux-single with IronTorrent data. We check several runs with QIIME1, an other demultiplex tool and the raw file like you and always we found more hits with QIIME2 tool. look here: Problem with cutadapt demultiplexing of IonTorrent data (Sorry I made the text to long for a forum discussion)