Oh of course.. Its a really silly issue. Turns out both of the Gneiss problems I had (this one and the one posted earlier: QIIME2 view of regression summary empty CSV) were related to the same issue.
I have posted a reply on this post -- its still pending, but hopefully gets approved soon.
In summary, I was trying to generate the regression summary using a metadata file that contained more samples than those i was trying to compare.
I had generated the balances and hierarchy files using a filtered features table. When I went to generated the regression summary, I would get the above error. However, when I used a metadata file containing only my samples of interest, it worked. As with the FDR table in the other post.
I'm pretty new to QIIME2 and do not routinely do these sorts of analyses, I'm simply running these analyses for colleagues who do not know how to use linux, so perhaps this was a newbie error. I've learned quite a bit over the last few weeks - the documentation is very well done and this forum is an amazing resource. So thank you for that!!