If the sameness of the same is the same, and it sounds likely, there's only a few things it can be. One, is a nut that's too high - when you press the string(s) down at the third fret, how high is the clearance over the first fret? (A capo helps here).
How is the relief, that being, press the string(s) down at the first fret and last fret - how high are the strings riding over the tenth, twelfth fret... capo obviously helps here too.
Does one neck have some really, obviously worn-down frets, i.e. big flat spots, more than 1/2mm wide...
If it's only on open strings, the strings aren't coming off the leading edge of the nut, but some ways back.
All of the above are relatively easy fixes, but they're each a different fix (and the worn frets require a level crown n'polish, which is only easy when you know how). So bang through those and let us know... if it's "E - None of the above" it's got to be a playing/adjustment issue of some sorts, the height of the strings above the body vis-a-vis the way you hold your hand around the bridge, the shape of the body affecting the angle(s) you hitting the strings at, etc.
Two things that I personally do on my own guitars, that are just as "wrong" as can be, are:
1) When I set the intonation, I use both the comparison of the 12th fret harmonics to the 12th-fretted notes, and the 19th fret harmonics to the 19th-fretted notes, and average the two or actually lean more heavily towards one or the other, depending on what I'm trying to achieve - these two measurements can be surprisingly different, and the heavier the string and the higher the action the further apart they get. I know that's ridiculously, unhelpfully vague, but I always have at least two (more like four) guitars specifically set up for high action/open tuning slide guitar. I still want to be able to do some low fretted bass note runs and the Sonny Landreth-style mixed slide+fretted notes behind the slide things, and when you get to 13-56's, open E, with 1/8" action at the 12th fret, well; there's a whole LOT of compromising to get any of that working.
2) What's completely Satanic/should be shot at high-noon is, I set my intonation once the strings are a little bit settled-in/settled-down/worn-out/used... I understand that in order to be perfect, you should always use brand new strings - and your intonation will be perfect - from the time you put on new strings, until 1/2 hour later. And then your intonation will be off, and getting worse and worse and worse, right up until you put on new strings again. Which is just dandy if you're Carlos Santana or Keith Urban and you have a little army of little people following you around changing your strings and adjusting your intonation and coordinating your fashion statements, but the likelihood of me ever picking up a guitar with brand-new strings on it is... statistically, pretty slim. Every once in a while I have a reason or two to want something to sound really good so I'll put on new strings, but jeez - even completely setting aside the cost, it would take me at least three - five hours a day to change all the strings on all this stuff and get them all settled down enough to sound their best every single day - yes, a "D10" pedal steel guitar is what it sounds like - 20 strings of it's very, very own! :toothy12: I have to be obstinate AND fairly lucky to carve five hours a day playing time total, much less string-changing time.
Do you own your stuff, or does it own you...(?) :icon_scratch:
So I'll set the intonation once to do whatever recording I have in mind, then wait a few/several days to set it again. Strings do most of their settling within the first few days of playing, fortunately. When I read these stories of modern-day guitar "greats" in the studio, changing their strings not just every day; or every song; but changing their strings for every SOLO;
A) they sure as hell ain't changing their OWN strings;
B) Nickleback and Maroon 5 suck.