Intonation yes... Things to consider:
1.) Only checking intonation the classical way (12th fret harmonic vs 12th fret fretted) is not always enough.
I tend to check intonation way more thoroughly on my axes, with many, many reference points throughout the neck.
2.) If you use thinner strings, you may indeed be pressing the notes slightly sharp down between the frets,
or even slightly "Micro-bend" them when fretting without really thinking about it.
3.) And this is often overlooked. If you have a tad too much bow on the neck, and action that is not
really low, you WILL push the notes sharp especially in the mid to higher parts of the neck, since the
distance the string has "to travel" before making contact with the fret will be equal to bending a note
many cents of pitch. Remember, the placing of the frets and "theoretical" intonation is based on a string that
is completely flush against the fretboard and with zero relief. This will result in the best intonation, but will of course
make the strings choke. Thus we always need some relief and string height to get a clean tone.
This can be compensated by moving the bridge/individual string saddles further away from the neck to compensate
(thereby lengthening the string portion between the fretted note and the bridge).
However, with high enough action and relief, you run out of options. You simply will not be able to compensate the upper
fret intonation without negatively impacting overall intonation at the lower frets.
These are one of the reasons I use 0.11-49 strings, have a very slick relief and quite a low action.
The larger frets still give me enough grip on the strings for perfect control when bending,
and the heavier gauge means I can go lower and slicker without "choking" the notes.
Thus, you can actually a better intonated, better sounding, slicker playing instrument with heavy gauge then light.
It comes down to very, very, very meticulous setup though. The stock PRS setups are very well suited for all-round
playing and intonation with 0.10 strings (or even 0.09), but when doing setup work on PRS guitars with 11's,
I always tweak them quite a bit. And the proof is in the pudding. Having tones of great players test drive my PRSi
at the trade shows around the globe, and every single player commenting that they have never felt a more
"effortless" instrument (even legato meisters like Tom Quayle for one) is a testament to this.
Not blowing my own horn here, but have been fine tuning this setup since -94 on every conceivable guitar brand
so I got it down by now :flute:
