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   1.  Players have different needs and expectations from an instrument. There is one adjustment that is universal, regardless of playing style (slide guitar excepted) - the string height at the nut, but to a degree, neck relief can vary from instrument to instrument, overall string height can very from player to player, and string gauge is a personal thing, which affects every setting. .

    2. The climate an instrument is stored in affects the overall set up.
Wood absorbs and releases moisture. Guitar necks and acoustic guitar bodies swell and shrink with fluctuations in humidity. This causes subtle and sometimes dramatic changes in string height and neck curvature.In the ideal scenario a guitar is always in a place where the relative humidity is around 50% and the temperature is 75 degrees. In reality, this is rarely the case. While a number of makers require their distributors to store and show guitars in a climate controlled room, in reality not all do. A guitar set to close tolerances is going to be affected by any changes in humidity and temperature. So it is not in the interest of the manufacturers to fine tune a set up.

   3. Modern factory's make a guitar in a matter of hours.
The precise adjustments that are involved in a thorough set up can take an hour of a technicians time. Big manufacturers just can't devote the time to fine tune the settings. Not to mention the fact that a good set up person can probably make better money outside the factory .

   4. Even a "new" guitar may have been sitting for a while before you bought it.
Guitars "settle in" over time and often need adjustment for this reason alone. .

    5. Some new guitars don't need a complete set up, just an adjustment.
Many guitars come out of the factory with a good set up but not a great set up, this combined with a seasonal change, or a shift of string gauge from what the factory installed, may necessitate some minor adjustments

   All of the above reasons contribute to the fact that a new guitar may need to be set up. But don't despair, getting a guitar set up and periodically adjusted is just a fact of life for a string instrument .