Question: I have changed strings, corrected neck relief etc, on my Les Paul and tuned and checked intonation using a Peterson strobe tuner, but when I play I'm hearing strings out of tune and intonation problems. Also I play with 10's with a wound 3rd string. Any thoughts on what's causing this?

Edit:
I have had a fair amount of experience in setting up guitars and on this one I checked the frets with two separate straight edges along with a notched straight edge to check the neck separately. I checked the intonation open, 1st fret, 12th fret and a harmonic on the 12th fret. All recordings sound in tune. Only certain strings appear to be out (they mostly sound flat to me) usually it's the d and g strings that sound out of tune. When playing I have noticed that if I adjust one then it will have an effect on how the other sounds.
Thanks so much for your thoughts.

Answer: 
[This article](https://www.ncbi.nlm.nih.gov/pubmed/20739892) seems to suggest that losing intonation with age does indeed happen. However I have never witnessed what you are describing even though many of the musicians I know are quite old (over age 60). I recommend you go to a doctor for a hearing exam just to be sure. Regardless of how often something happens in general your case is unique. 

I am assuming that if you went as far as to use a strobe tuner to test intonation that you checked the intonation of individual frets. Have you tried listening to different guitars? Do your favorite recordings sound in tune? IF they do then the problem might indeed rest in your guitar rather than you. 

Update:
If recordings sounds like they are in tune then it probably isn't your ears that have the problem but rather the guitar(s) you are working on. 

I'm no luthier, but on the stringed instruments tuning stings usually affects the tuning of other strings. The tuning process is done repeatedly until all of the strings are more or less in tune. Even if you are experienced it probably won't hurt to take your guitars to a shop. While you're there have a go on other instruments in the store and have them check yours out. 

I'm glad recordings still sounds in tune to you. That suggests that your hearing probably isn't what's at fault in this case.
If you, at almost any age, can hear that something's out of tune, for whatever reason, then most likely it is out of tune. Listening to anything else, I would imagine you feel it's in tune, especially recorded stuff. 

So, there's probably nothing wrong with old ears. Certainly hope not - mine aren't as young as they used to be, but I wish I'd been sensibly wearing earplugs far more! 

I suspect the accuracy of the intonation process, with due respect. Or the fact that something has gone awry with the guitar. New strings can take a while to settle in, changes in temperature and humidity will take their toll on tuning also.