That's what mine was doing too. It worked, and the pickup split switch worked, but it didn't have the output it should have. What confirmed to me there was a problem was when I rolled down the tone control to 0, and the neck pickup's output dropped to nothing even though the volume was at 10, but the other pickups sounded as they should, darker but with a lot of output volume.
I got confirmation from PRS this morning that the pickup on mine does need to be replaced, so, hopefully, it'll be on its way home by next week. I'm not happy I had to send it in, but, all in all, working with PRS support has been fine and if I ever need to send in a guitar for a similar situation I'll be less nervous. I'm in Arizona, so shipping added some delay, but both repair shops I use locally are running about three-month backlogs, so sending it to PRS has actually been the faster path to getting it fixed.
I don't seek the eye candy that their maple caps tend to have, but I do want the mahogany body and neck, maple cap, and rosewood fingerboard. That said, this one has grown on me…