Hi @Nicholas_Bokulich -
Thanks so much for your advice. I realized I had done something stupid in an earlier step, and figure it might help people if I share it here.
We used 2x300bp paired end technology, so I thought naturally I should join the paired-end reads. However, due to variation in the ITS gene sequence length (which can be upwards of 800bp), the reads actually have a pretty high chance of not joining. I re-did the analysis using only the forward reads, and got way better results. Some samples communities were still classified only at kingdom level, but a BLAST of sequences shows that there is not a high percentage match to any one phylum (or lower level), and the conservative kingdom level classification is probably best.
Hope this helps someone out there 