#1
So, whenever I tune to drop C, I end up tuning the low C string down just a bit lower than the tuner says. Otherwise it just sounds out of tune to my ears. I thought intonation was to blame, but even when playing an open C power chord, it sounds better when i drop the lowC for a few cents. I dont really seem to have that problem when I tune to D standard, or even if i do, its much less noticable. And when i play in drop C it sounds fine when i do single not riffs, but power chords just sound a bit of, unless i drop the low sting just a smidgen.

So, what gives?
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#2
it means the entire intonation of your guitar is off by a little bit not just the one string.
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#3
Could be intonation, also could just be the way the string reacts when it has lower tension. When you tune strings, do you hit them soft or as hard as you would while playing? Lower strings tend to pitch up when you hit them hard.
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#4
You need to remember that strings go sharp by the very nature of plucking them. And the harder you pluck the strings, the sharper they get. This is the key phenomenon for why all musical instruments in general are impossible to perfectly intonate. By forcing something to vibrate, you're imparting additional tension on the medium that's being vibrated and that additional tension alters pitch.

It's common for people to pluck strings lightly when tuning and setting the intonation, significantly more so than if they're playing the guitar normally. This is a mistake, you're going to be plucking the strings out of tune all too often that way. What you should really be doing is plucking the strings just like you would when playing the guitar normally when setting the intonation and tuning. That way you're setting the guitar up in a fashion that achieves the best compromise for the how you play it.
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