Phil,
I have exactly the same issue with my Ibanez RG1550.
Here's my personal view on the subject:
Every guitar has a resonance frequency -- its just plain old physics. Its just that sometimes the resonance frequency falls between the notes, and sometimes it falls on the notes. That's why some guitars are not affected, some are affected a little, and some -- like yours and mine -- are affected more seriously. But I think the vendors are not to blame, this is very chaotic; even small variations, for example in the wood structure, might move the resonance frequency around and no QA process can guarantee that a certain guitar has its resonance frequency where you want it, namely between the notes.
I cope with this by trying different string gauge and different tuning (A438-A444 as already suggested), hoping that it would go somewhere that it won't bother me. First time I found out about this, the dead note was on the A note, most severely pronounced on the high E-string, 17th fret, and it was awful. By changing the string gauge, using A438, and tuning 1/2 down, it moved to B (17th fret G-string on a Eb-tuned guitar) and it bothers me less there and I mostly ignore it. Sometimes I can't ignore it -- like in the Petrucci Made Easy lesson there's a sustain right there and I had to slide out in order to make it work somehow (https://www.guitarmasterclass.net/guitar_forum/index.php?showtopic=56873, around 0:24-25).
Moral of the story: I doubt PRS would want to change your guitar, but do give it a try. If not -- do not despair and try to cope with it by changing gauge, tuning, weights, blocking trem, basically everything the guys here already advised. Eventually you will mange to move it somewhere that's less of an issue.
And last and most importantly, I think there's a lesson to be learned by everyone -- one should always buy a guitar after manually checking each and every fret on each and every string for sustain.
Cheers and good luck,
-Val
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