So, what is your easiest solution if the strings are binding at the nut? Take in for a smoothing nut file job? Lube? Other... I tried some nut lube and it didn't seem to help at all. Might need to go to the next level.
(and yes, I realize how funny that last part is when said out loud :tongue: )
Well, mine is a brand new SE Custom 24, about a week old, 2014 model, in vintage yellow. Very beautiful and nice guitar. It did the same thing. I know because I specifically checked it this morning before putting on some new NYXL strings. Sure enough, it did not return to perfect tune after using the whammy only slightly. About three of the strings were quite far off.
So, when I put the new strings on (one at a time, keeping the guitar in tune) I made sure to take the string that I had just removed and run it back and forth in the nut slot repeatedly to open up the slot a little. Three or four strings definitely were pinched in the slot when I went to remove them. So I did a good job of running the strings back and forth until the new string would fit in without resistance. I then put some powdered graphite in the nut slots and in the grooves of each saddle, and put the new strings on, keeping the guitar in tune, one at a time.
Then I tested it out. Wouldn't you know, after applying the tremolo, even rather gently a few times some of the strings still did not come back into tune. They were a lot closer but not near being in perfect tune.
Thinking it over, I decided to loosen up the identified strings, remove them from the nut slots and slide a piece of folded fine sandpaper against the sides of the nut slots, one at a time until I got the string to come back into tune perfectly after applying the tremolo. I was careful when doing this not to sand the nut slots any deeper, but to just sand against the sides of the nut slots. I applied more graphite and repeated this until I got every string to return to perfect tune. I think it was three strings, possibly four, all wound strings. The "B" and "E" did not bind.
It was a relief to find that I could correct this problem myself, to my satisfaction, because it was definitely not coming anywhere near back to perfect tune when using even the most gentle tremolo action.
The guitar also stays in tune after doing moderately heavy bends repeatedly on three or four strings.
One thing I noticed on another of my guitars, an SE Singlecut Tremolo guitar, is that after I put Grover 406C mini locking tuners on it, that it stays in tune for days, even weeks if not played every day. I'm sure that with extra hammering on it that it would need to be fine tuned after every couple songs, but under normal play it stays in tune extraordinarily well. I'm going to get some more of those direct drop in tuners. The smaller buttons look just fine to my eye, no problem there. I could try a different brand though, but they would have to be direct drop in and, of course, not hit the headstock when turning them. There is not much clearance on the "E" strings for tuner buttons.
Anyway good luck. If you decide to use fine sandpaper (220 grit, approx.) be careful not to sand the nut slots "deeper". You do not want to do that - you just want to widen the nut slots a little at a time, try the guitar and if it still doesn't come back to perfect tune, sand some more, put the string back in and try again until you get it widened out just enough to come back to perfect tune. Try to sand lightly with precision, but just enough force that the sandpaper "cuts" into the nut material. If it's a black nut you will see the black on the red "garnet paper", regular reddish sandpaper.
Others here may not approve of the method that I used, but it worked for me. Also, my guitar is not a multi thousand dollar USA PRS either. On the other hand, even if it was, I would be very cautious to what ever so-called guitar tech I took it to, if you know what I mean. I know a couple real good guitar techs in my area; one is close and the other one is about 85 miles away, one way. These other so-called guys I will not trust to do anything other than very simple work, if any at all. I think I can do a better job myself in most of these cases, even intonation, soldering, trouble shooting electronics, installing upgraded pickups, tuners, etc.
Furthermore, I'm sure that no one, at the factory or otherwise, touched up the binding nut on my new SE Custom 24 before I did. All else aside, the slots in the nut were just plain too tight for the strings. That seemed very evident, cut and dry. I would not expect this on a costly USA guitar.