DL can't issue PDX-ATL-SJU in C
 

Perhaps this is a common thing on Delta, but I've never encountered it before. I used the website to book PDX-ATL-SJU r/t in F/C, and just before I hit the "buy" button, I noticed that the outbound ATL-SJU segment was in Economy, rather than "Business", so I called. After many minutes of holding, escalation, and so on, I was told "that segment [ATL-SJU] is sold out in Business". Well, fair enough. But then I looked up that flight independently, and of course it is completely empty in First/Business -- full inventory available, when booked from ATL. But PDX-SJU, not available. I tried all variations of multi-city bookings, etc -- no dice.

I called back, and said "I don't care what the price is, please book me in First from PDX-ATL-SJU". They couldn't, wouldn't, and seemed to think it was unreasonable of me to ask. They kept talking about how they can't book "point-to-point" flights.

In the 40 minutes or more this took me, I was able to pull up a (slightly less desirable) flight on American, PDX-DFW-SJU, in First for about the same price.

But what gives? Why couldn't they build an itinerary that used available inventory and sell me a ticket on it? I know I could do it with two separate PNRs, but why?

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.

Worst case in this situation should be that you can purchase two separate tickets, but that will be expensive and could cause trouble in IROPs.

My understanding of married segments does not explain this.

Married segments means that inventory on A-(B)-C might not be available on A-B and B-C, or vice versa.

But one can always book A-B B-C with a fare break at the summed price of the two legs.

As such, the OP was just a victim of brain dead service.

Can any of the routing guru's clarify if my understanding is correct?

I verified that I could book PDX-ATL r/t, and separately ATL-SJU r/t (at a substantially higher combined price), but I wasn't able to book it on a single PNR, even with multi-city routing, and even on third-party sites. It simply bumped the outbound ATL-SJU segment into coach.

And as brain-dead as the service was, I sort of believe them that they couldn't price that ticket without splitting it into two PNRs. In the end I bought the flight on American, and Delta lost an F r/t fare.