Does it go sharp, flat, random one or the other, or random bits of both across the strings?
Did you get it new? Did the vendor (dealer or store or guy you bought it from) do a proper set-up?
Did you just put new strings on? How much string is wound around each post? Shouldn't be more than a full turn or so, preferably between 1/2 and 3/4 for me. The advantage of locking tuners...
Does it have factory strings (010s) or is it set up with 011s? Does it go back in tune (or at least closer) if you bump the trem just a bit?
As you tune, do you hear the strings go "plink" or "ping" every now and then? This indicated binding in the nut.
I have found all my Newer PRSi to be a bit tight so to speak before you go to far just play it HARD use the trem a bunch mine have all settled down pretty quick
Yeah, Musician's Friend has pretty good pricing at times, but their "set-up" might only consist of "open case, check guitar looks new, close case. Oh yeah, check case." I got my P24 from them, IIRC (my memory sux..), and it played great out of the box, but I did lube the nut and tweak action and whatnot, also IIRC. If the guitar was "open box" it might just be "dusty" and need a work out to get back into the groove.