As an avid reader on FT, I'm pretty familiar with the dangers of split PNRs. Here's what transpired with me last week...
Tried to check in online on 11/28 for our 11/29 flight: DCA-ORD-HNL. My partner and I were waitlisted for upgrades (with miles). I was unable to check in, and it said I had to see an airport agent. Normally, I would have just called, but we were going to be driving by IAD on the way to see family so I thought I'd see what the deal was.
Went to the counter, and explained that I couldn't check in online. It took at least twenty minutes and four agents to check us in. They were actually nice about it - we were joking about the horrible system, married segments that needed to be "divorced", etc. Got boarding passes but as we walked away, we noticed we were now on different PNRs, which I did NOT want to happen since the upgrades probably weren't going to clear and I didn't want any trouble on the return in case of IRROPS.
The agent who had originally been nice completely changed her tune and was done with me - she told me I had to go to the "originating station" (DCA) for anything else. Needless to say, when we stopped by the counter at DCA the next day, there was nothing they could do but apologize and use the system as an excuse.
I'm still ticked off that they had to split our PNR just to check us in, but even more upset about the fact that I was flat-out lied to about the whole thing. I'm all too aware of most of the existing system limitations, but there's still a customer service element in how you deal with them that was sorely lacking here.