I just recently traded in a PRS for exactly this issue (among others). Don't get me wrong, these are definitely world class guitars, but there are issues.
I always wanted a Les Paul, that was until I tried a PRS. I was sold the first time I picked one up. I'm a strat player basically, so the way if felt to me was much nicer than the Pauls. Anyway, after the initial "wow" of owning a PRS wore off, I started breaking strings too. After the set that came with the guitar, which I presume were factory PRS strings, I put on what I use on all my guitars - Ernie Ball Super slinky's. I've been using them for over 20 years, and they never let me down. The first set I put on popped a G string after 20 minutes. The B string went 10 minutes after that. I figured I had to have a bum set of strings, so I replaced them, and the same thing happened - over and over and over again.
There was no burring at the saddles, no problem with break-over angle, no issues with the guitar at all, as far as I could tell although to PRS credit, they offered several times to replace the saddles sight unseen.
Here's what I came up with. As a strat player, I'm used to the contour where my arm goes over the body. It's smooth, and obviously affects the angle at which my pick attacks the strings. The PRS didn't have that. In fact, it has that little lip the whole way around the body where the top is attached - the "binding". Well, the first time I played the guitar for more than an hour, my right forearm was actually bleeding from where it was going over that lip. Consequently I had to adjust my strumming angle, and I think that led to a string attack posture that messed up the strings.
I was able to get it to work acceptably by using the PRS strings. They are very expensive, but I was at least able to get a full gig out of the guitar sometimes - but never more than that. More often than not though, I ended up breaking strings 2 sets into the night. I couldn't justify holding on to a guitar that cost thousands of dollars and that broke strings with that kind of regularity. Whether it was my own playing style, or an inherent design flaw was irrelevant to me.
It may be that the guitar needs to settle in, or that you have to work with it a while, but in the end I was not too sad to see it go in favor of a Martin acoustic. Good luck to you - I know EXACTLY how frustrating it is.