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: 
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.
Adding to the answers given before I'd like to mention the following:

From the theoretical point of view Guitar tuning is much more complicated than piano tuning. Or in other words: It is more a compromise than tuning a keyboard instrument, as you have to consider each fret separately and simultaniously for all strings. This may be the reason that the 12-tone equal tempered tuning (short 12-tet) has been first reported in the wester music tradition as the solution to the problem of lute division.

As a secound point is related to just intonation. You can express the sound of one string by different frequencies. As a good approximation you can consider the inner ear as a gammatone filter bank with 3000 to 4000 frequencies, a Fourier series is often resonable, too. A just fifth/fourth as the difference between g and d is not very robust against mistuning. According to some authors (e.g. Martin Vogel) the just noticable difference of two sine tones (about 1-2ct) is also noticable in the timbre of two strings tuned a fifth apart when played together. This explains why the two strings interact with each other.

The third thing is related to the aging process you are referring to: The natural learning curve is not linear. At the beginning you are lerning to understand the problem. This is the first noticable phase of learning. Later on you learn from variation. This means that you do not notice any progress. I assume that you try to avoid variation in the tuning result. So collectiong variation might be difficult and a long process. After you collected enough variation there may be the point where you suddenly reach a new quality of your task – in this case the listening to the tuning of your guitar.

Finally I'd like come back to the physical behaviour of your guitar. Preferably the corpus has no undamped resonance frequency. I own a guitar which has a relatively strong weakly damped resonance frequency, which makes it hard to tune a particular string. Depending on your hearnig skills you may even notice the difference in the degree of different partials of your guitar strings. Sometimes these can be caused by the strings themselves (e.g. nylon strings may loose homogeneity over time).

As a conclusion your description sounds to me as if you somehow got another instrument, your instrument needs some maintenance (e.g. new strings), or you improved your hearings skills over time. It might be also a combination of these things.