Sounds like a married segment issue, not sure why they wouldn't just book it with the fare break. You should be able to construct the fare yourself using Google flights and the multi-city option (delta.com's multi-city search is kind of wonky these days). Specify business fare and PDX-ATL and ATL-SJU as separate flights. Without knowing your dates, not positive this will work, but I was seeing something similar for return flights SJU-PDX on Jan 2nd and was able to get around it with the above technique.