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Additional conditions added via joinWhere and joinOrWhere were not being honored on MysqliDb configurations with prefixes. A bit of debugging revealed that in _buildJoin, the table name stored in _join had the prefix, but the one in _joinAnd did not. This caused the condition isset($this->_joinAnd[$joinStr]) to fail and never consider any of the extra join conditions.
Problem stems from joinWhere commands being keyed by the raw table name as provided, without conditioning it like the way join does it.