The hidden accounts that are appearing with zero balances don't have a management fee assigned. They are, however, children of a parent sub-portfolio that do. Not sure if that makes a difference. Also, these sub-portfolios are linked to other sub-portfolios.
Here's what's interesting: If I run the report over "last quarters" date range, I don't see the hidden accounts. But if I change the date range to "current quarter" (and not change anything else), the hidden accounts appear with zero balances.