Hi @rlhughes,
It’s hard to troubleshoot this properly without seeing any of the commands you’ve used but I’m guessing the issue is just the wrong biom format being used. You may have to convert your biom version before importing. See this post for an example and more details.
Also, if you are using a windows system R and importing to a mac/linux qiime (maybe through a virtual machine) you might find this recent post useful too regarding changing line endings.
If these don’t resolve your issue could you please provide us with the exact commands you’ve used since exporting the biom table out of R.