Strings can be a major player in these kinds of things. To my knowledge, good high quality strings are not typically difficult to tune and intonation seems fine - when fairly new. Old strings are a different case. A couple questions:
- How old are the strings that are on the guitar now?
- Have you had this issue with other brand strings of the same gauge?
- Is the tuning issue better, worse, or the same as your chosen brand of strings?
- Are you in tune BEFORE using the capo?
- What type capo?
- If the guitar is in tune without capo, do you have to re-tune after putting the capo on? (try to avoid this)
- Have a GOOD repairman (if not the builder) look it over every year to 18 months, let them give it a once over, cleaning, re-string. Costs a little money, but good for them to stay in business and keeps your instrument in good care.
- Changing the strings is something folks tend to avoid. They don't like to do it, costs of strings, etc. Folks buy coated strings so they don't have to change them as often. But I think it's important to do exactly that, change strings regularly. Coated strings are designed to last longer to avoid changing, but even they need changed at times too. Some if not most intonation issues can be caused by fatigued strings.
- Getting your guitar in tune before capo use is vital to playing in tune with and without capo use. Once the guitar is in tune, capo use should be able to happen without turning the knobs. Capos actually cause the pitch of the strings to be sharp because of the pressure placed on the strings. Some capos are better than others for this, and placement is important too. Placing the capo as close to the fret is best, just behind the fret. More pressure = more sharpness / detuning occurs.
- The nut and nut slots are vital to how a guitar plays, sounds, and intonates. Slots too deep results in buzzing. Slots to shallow results in harder action to play, and excessive intonation issues - with and without capo use. Repairmen / luthiers can examine and adjust this.
- Neck angle / relief is also vital to playability and intonation.
I happen to use Gallagher Guitars and Rockbridge Guitars. These are two small companies who hand make their guitars. They don’t have string companies in the back buildings, or case makers, or anything… they make guitars. Great guitars… to me.
I also use D’Addario Strings, which are made by D’Addario in their string manufacturing buildings, with D’Addario on the package. That’s my preference. They are the best… for me.
You may want to try several brands of strings to see which you like best. Make sure you use the same gauge strings as is on your guitar, as it is set-up for a particular gauge. Don’t choose your strings purely for the fact the brand name is the same as your guitar builder.
In the end, it’s one man’s opinion. This is mine here and my preferences, yours for your preferences. It’s all good… but see if you can upgrade ‘good’ to ‘better’, and better to best.
I hope this helps. Stay tuned!