Lately, I noticed that my excellent acoustic guitar is always sounding off tune even when I have tuned it with keyboard and even electronic tuner. Another thing I noticed is that when I play the individual strings or notes or run a scale it sounds ok, but when I play a chord it sounds so off and unpleasant. Is my guitar damaged?
Assuming that the strings are not worn out, the two most common causes of a guitar with proper intonation developing problems with intonation would be:
These problems can be caused by the expansion and contraction of the wood in the neck and the top of the guitar due to changes in temperature and humidity (in exposure to great heat or cold, or exposure to extremely humid or extremely dry air). On the other hand, if the guitar was not built correctly, flawed wood can warp and glued joints can come unglued. Or if there is too much tension on the top and the bridge due to the neck being set at the wrong angle when the guitar was built, a guitar can start to develop problems as well.
A qualified guitar repair technician can often repair these problems. Your neck's truss rod can be adjusted to correct too much or too little relief in the neck; your bridge can be re-glued or have modifications made to its saddle to compensate for intonation problems. You should have your guitar inspected by a repair technician to determine what the problems are and how to address them.
There's tuning, and then there's intonation. The frets of a guitar are laid on the fretboard according to a very precise mathematical calculation, based on the full length of the string from nut to saddle. On an electric, the curve of the neck, the height of each string (or all strings), and the distance from each bridge saddle to the nut can be precisely adjusted to bring the instrument into proper intonation. On an acoustic, all you have is the neck adjustment, and some control over bridge height, so this is tricker.
The basic problem is that, when you fret a note, you change the geometry of the string. You shorten its speaking length by placing it against the fret, but you also increase its tension because you're pulling it down to the fretboard. The guitar's fret placement is carefully designed to accomodate that, but it will only do so perfectly if the instrument is adjusted and played exactly as the luthier who built it expects you to. If it's too far out of adjustment, you either won't tension the string enough at a certain fret and the note will sound flat, or you'll tension too much and it'll pull sharp. Acoustic guitars, especially the mid to high-end ones with solid tops, are also weather-dependent; changes in relative humidity can throw off these minute details enough to make a noticeable change in the intonation.
The first thing to fix is humidity; guitars, especially solid-tops, like being kept at a relative humidity of about 45-50%. The actual humidity in which you store and play your guitar can vary widely, from as low as 5% out in Phoenix or Las Vegas, to 95% plus in wetland areas like the Gulf Coast. Indoor humidity versus outdoor can also vary, even between rooms of your home.
To check for proper humidification of your guitar, take a ruler or other straightedge and press it against the last few frets of the neck, then slide it out until it reaches the bridge. The straightedge should just barely clear the wooden part of the bridge and hit the saddle. If the end of the straightedge hits the bridge itself, the guitar's too wet and the top has bowed out, raising the strings; if the edge hits high on the saddle, it's too dry and has sunken in, lowering the strings.
To humidify a guitar, either go grab a sponge humidifier from the local music supply store, or take a sandwich baggie, punch several holes through it, then add a damp (not dripping) sponge, seal the bag, and place it in an empty area of the case; good places are in the neck area, between the guitar's cutaway and the case, or to either side of the heel of the neck. Real humidifiers are often designed to hang between two strings down inside the guitar; you can try to replicate this position with a homemade humidifier, but be careful not to let the humidifier come into prolonged contact with any bare wood inside your guitar. To dehumidify a guitar, take out all the humidifers and the guitar itself, then take a hairdryer on high heat and go over every inch of the lining inside the case, drying it out as best as you can. Then, put the guitar back in the case, and add some silica gel packets in strategic places (same places you'd put a humidifier).
Next is the neck relief. Once the guitar's properly humidified, hold it by the body and sight down its length, from the bridge down along the neck on both sides. The neck should have just the slightest up-bow, giving the lower frets the needed string clearance to avoid buzzing, without the strings being too high. Exactly how you adjust the neck depends on the guitar; usually it's an Allen key either just inside the soundhole, or under a cover on the headstock. Tightening the neck will increase the tension of the truss rod, bending the neck backwards; loosening it will lower this countertension and allow the strings to bend the neck upward. To check for proper "relief", either hit the hardware store and pick up a set of "gap feelers", or find yourself a cutting from a .010" guitar E-string. Put a capo on the first fret, then press each string one at a time at the last fret. Slip the .010" gap feeler or the string cutting between the string and the 8th fret; if it passes through easily, you have too much relief; if it doesn't pass through without pushing up the string, you have too little. Perfection here is when the feeler or cutting passes under the string, catching just slightly on the string's windings.
With these two taken care of, pick the guitar up and make sure it's still in tune, then play a few fretted notes for the tuner and see where you are. If you're still sharp, you may be pressing the note sharp with too much pressure from your fretting fingers, or plucking too hard causing the string to tense sharp as it vibrates. You need just enough tension to keep from buzzing. If you can't make it work, consider replacing your strings with the next thicker gauge (if you play .012-.053 "lights", try .012-.056 "light-mediums" or .013-56 "medium", depending on which strings are trending sharp). Conversely, if your notes trend flat, you may have too heavy a gauge for your playing style and need to lighten them a little.
Lastly, if it's still not tuning properly for you, examine the bridge and nut. The bridge is under a high amount of tension (approximately 20 pounds from each string in standard tuning) and this tension can cause the glue and anchors holding the bridge in place to begin to fail and pull upward. If you see the back side of the bridge coming clear of the top, slack all the strings and take the guitar to an experienced luthier for repair.
Also examine the nut; the nut has slots which space out the strings evenly and place them at the right height above the frets. If these slots are too deep, the open string will be too low off the frets; the usual symptom is that the open string will buzz, but other symptoms include lower tensioning of fretted notes, meaning they'll be flat. Conversely, a nut with the grooves too shallow will have a higher string height over the fretboard and you'll be pulling notes sharp. A nut on a guitar that's been well-loved can be worn irregularly, so some strings trend sharp while others are flat. A luthier can adjust or replace the nut for you as well.