Thanks @thermokarst for deploying an older version.
We've seen that the SVD operation in the newest release of numpy and scipy are broken: np.linalg.svd gives weird output · Issue #13401 · numpy/numpy · GitHub
What this means is that all beta diversity calculations involving svd (i.e. pcoa), in addition to the balances will output wrong results using qiime2-2019.4
The newest qiime2-2019.4 environment files should avoid this issue by pinning numpy to an older version. So make sure your qiime2 environments are up-to-date if you are using qiime2-2019.4