Not a super detailed explanation, but I know that my guitars usually take about a week to "settle in". I was worried that my Strat was messed up until I remembered what my old bass instructor told me "You have to let your lady settle in before you start thinking she's crazy".

A guitar that sounds great in the temperature and humidity controlled store may take a while to adjust to your home (I live near a river so I know my home's humidity is radically different than the store I go to).

Just F.Y.I. my Strat took about ten days to settle in, now she only need an occasional adjustment to keep her playing the right notes.