I can imagine someone telling a story about the past (the Perfect tense generally being about things that have finished happening, as I understand it). For example: "When I got back to the meeting point, Jim wasn't there anymore."- "Where had he gone?"- "He had gone to put more money in the parking meter".
I kinda agree... It just sounds strange. You could say the same in Dutch: "Waar was hij geweest?", but it doesn't make sense... You could just as well say (and we do :)) "Waar is hij geweest?" (where has he been / vart har han gått (?)). In my opinion, if someone has been somewhere in the past, he has still been there in the present... Actually my question is, would someone actually use this sentence in Swedish..?