I've noticed that a lot of guitars seem to go out of tune when they have a capo on. I don't know if this is a problem with the neck of the guitar or with the tension of the capo, but it seems like a lot of guitarists have just gotten used to the sound of their instrument being out of tune in certain keys.
Eamesuser, could this be part of the problem for you as well?
Capos are an imperfect solution.
All guitars (except for those with ridiculous fretting schemes, although fanned frets aren't a terrible idea) need to be intonated. Because you're dealing with six strings of slightly different tensions with the same basic scale length (that you adjust) and the mathematics of fret placement have to cater for all strings, intonation is a compromise. Typically, you intonate the open string and compare with the 12th fret - which inevitably means that at various points along the neck there are slight deviations from 'perfect' tuning, most noticeably around the 4-8th fret and 16th fret, etc.
When you're using a capo, the effective scale length changes and you don't re-intonate the guitar for that shorter scale length. So what happens is that the guitar
is actually slightly more out of tune than it is without a capo. You cater for this by having the capo as close to the frets as possible (that does improve matters, if the capo is at an angle then you don't have such a clean fret 'break point' and the intonation can be even worse. A really tight capo will also pull the strings sharper and out of tune.
So yes. Guitars are complicated with intonation. The biggest bugbear for me is when gigging guitarists change their string gauge and then don't re-intonate. That causes a lot of issues. The other issue is a poorly cut nut. My Strat has a pretty poor nut (my fault) and tends to be slightly out with open chords. It's not noticeable but I know it's there...
EDIT: A 'perfect' guitar solution would be a fretless guitar played flawlessly. That doesn't happen in real life. It's also interesting that violinists when playing solo prefer a Pythagorean temperament over the modern temperament and have to adjust when accompanied. We can go even deeper into this, too. Modern Pianos (which tend to define the system that we use) use what's called an 'equal temperament', although only ostensibly. In reality, they actually stretch the temperament out at the top end because it sounds 'better'. 'Just' temperaments (the ones we used up until the early 19th Century in general) sound 'better' but don't work across all keys. This is why old keyboard instruments and wind instruments in traditional tunings (harpsichords, some early Pianos, etc) sound
fantastic in some keys and
terrible in others. Typically, 'D' and its related keys were favoured because it worked well with trumpets (which had no valves at the time).
So, around Beethoven's time, modern temperaments were developed that were ultimately a compromise. Everything sounds quite good but nothing is
fantastic. The musical benefit of this is that you can change between keys at will without having to worry about how the instrument will sound. Beethoven's 'Well-Tempered Klavier' was a response to this, selling the benefits of the new system.
Anyway. I need a cup of tea. Sorry for that, I don't know what came over me.