Take a look at salesperson RD in the OE sample data - she has a credit note that appears properly.
In my experience, the standard commission report is inadequate except in very unusual circumstances. I always write a report customized to the client's needs, usually in Crystal Reports. This is especially true if the commission rate varies by item, or if the commission is earned when payment is received, not when the order is invoiced. In these cases, I use SalesAnalysis as the database on which to base the report.
The ability to generate a commission report based on payments received is one of the most sophisticated features of Adagio; there is nothing else out there in the price range that can do it, and I find it to be a major selling point of Adagio (sometimes it drives the whole sale).
Steve