This is Marianne. She's 17. She's a standard US strat. Officially retired, but I still play it every now and then.
 

 
I've thrown her all around, smashed her against a tombstone (repeatedly), dropped her on concrete several times, spilled the equivalent of four or five 6 packs and 2 bottles of red wine on it, air travelled w/ it, walked on it, jumped on it, played in the rain with it, took her apart and put her back together, left it tuned in every imaginable tunings for weeks...
 
Intonation is still impeccable and exactly as it was when I first tried it in that music store back home. Not even the slightest adjustment.
 
OTOH...
 
I have two Epiphone Les Pauls, which I recently tuned down a whole step to re-record an old song of mine and kept tuned lower for a week while working on that song... I'm thinking that climatic changes probably also come into play. Anyway, those ladies are giving me headaches - I can't fix intonation at bridge level anymore, so I've had one of them sent to a friend of ours who fix guitars for a living - I'm not messing with the truss rod and neck relief or the nut...
 
I was thinking that this is what I get for buying Epiphones instead of Gibsons - but then I picked my Epiphone LP Junior - the $99 bolted-neck/unadjustable wraparound bridge/cheap nut and tuners wonder that accompanied me in my travels to Spain and Russia - in a regular suitcase w/ the neck unbolted and with an.
 
Guess what… No intonation issue whatsoever. :/
 
Is it a matter of set neck vs bolt on? Any other idea? I do taker really good care of those two LP man, more than I've ever taken care of any guitar...

Leo Fender was a genius.
 
 

Good intonation is achieved by correct nut, fret and saddle locations.
 
Dirty little secret ... I guess many "tone kings" ears are sure turning red.
Tuff stuff.

We have been driving around Orlando with a Go Pro. I had a flat base mount gaffed taped on the hood of a Volvo for 6 days.
 
Tuesday night I pulled the gaff tape off and had the vehicle owner stop at a hardware store where we bought some "Goof-Off".
 
I told him not to worry about his paint job. The Goof Off will not hurt it a bit and the adhesive residue will wipe right off.
 
Easy, breezy. Plus, I enjoy the smell of Lacquer thinner.
 
:-)

 Glad you found a solution Mike.
 
"Easy, breezy. Plus, I enjoy the smell of Lacquer thinner."
 
 Ehh. Never mind.

Maybe it's just a matter of luck. 

Adjusting the truss is nothing. May be hard to get on the truss the first time but after that no problem at all.
Loosen it or tighten it. I have just loosened mine a bit because of weather (or from changing conditions from where I bought it). The 1st fret and the 15th fret are held down and the thickness of a good business card is suppose to be at  the 7th fret when you look at it. I got a little more now, but since I did not pay $3000 or more or a little less for any guitar I have, it fits the guitar better for me. Set the bridge saddle locations so the 12th fret is in tune. (use a Snark or something. It is suppose to be the harmonic overtone, but to me if the tuning is off then so will be the harmonic. And afterall making the string do the harmonic takes a little practice to get.)
The bridge height may be adjusted some also to account for the guitar.
 
An expensive guitar should be better but all guitars are adjustable. I am still playing around with mine for the moment since I just bought the Epiphone. I will not say it is better, than a more expensive guitar or even as good. But fine the $2100 difference for the price of it between that and the Gibson (at least to me). Yes not as good as a more expensive guitar usually, but good enough.
 
It is not hard at all to adjust a guitar.
 
New one:

http://s1.directupload.net/images/131031/gncvwa53.jpg
 
and I could change everything out about (pickups, perhaps bridge, stopbar - not needed, and pots) and still pay someone a lot of money to do that and still to me not have spent as much.
 
Still I will wait and see and I have looked at it completely and adjusted the truss rod and look underneath the one neck pickup to adjust a slant it had and changed strings and actually been thinking to myself that at this rate, Gibson is going to have to move to China and set up shop somewhere near the Epiphone type gibson plant there.
 
?????
 
es-339.
 
 

Nice Epi, Spacealf.
 
I picked up this one almost 2 years ago for my 50th.  I have changed the bridge pick up out to a Gibson Classic 57 plus.  Now I need to work on getting a neck Classic 57.  As you say, it is not quite the quality of a Gibson 335, but it is not $2,000 difference.  In some ways, I feel it actually plays better than my Gibson LP Studio Premium Plus.  
 
 
 

Nice Big Sister there MakeShift! I can not come up either with the price difference and I still am allowing quite a bit of leeway for labor and if doing it myself, it does not even come close.
 
??
Oh, well.

Mine has push/pull coil taps also, the Gibson has the Memphis Circuit in it, but not push/pull coil taps (although they do not make that much difference on that guitar it seems). The sound is different then an es-335 but still Sweetwater had some Epiphone Les Pauls with Gibson '57 pickups and I think it seems to be a solid no hole Les Paul also that is sold out for $600 including case. Mine did not include case but still with it was $100 less.
 
If they get anymore in (and they do not look bad at all either although slightly different colors from Gibsons), it's hard not to have GAS for one of those perhaps also. (considering that should be about $1650 difference). (The Epiphone Les Paul).
 
Oh.............................the pain of it all!
 
Ya, the neck is different but actually I am beginning to like it better since my Gibson is a just a bit smaller in width.
Clunky hands and fingers I suppose.
 

Oh, back to Leo. Well, I have a Leo amp.