Negative distributions are not included on payment distributions.  By design, negative distributions on invoice records are considered "transfers" and are not reflected in the payment distribution.  Transaction distributions (i.e. Project distributions) on negative invoice distribution lines will not be reflected on the payment distribution.

Example
Invoice Distribution:
DR: 01-5000-00, CR: 01-2000-00 - Project 1000 - $100
DR: 01-5000-01, CR: 01-2000-01 - Project 2000 - ($50)
DR: 01-5000-02, CR: 01-2000-01 - Project 3000 - $50

Payment Distribution:
DR: 01-2000-00, CR: 01-1000-00 - Project 1000 - $100
DR: 01-2000-01, CR: 01-1000-00 - Project 3000 - $0