If a steel string guitar is left unstrung for several months it may very well take several days to settle down again properly once brought to pitch.

Now you have digested all of our advices, what is the situation with the octave? Is the 12th fret the same as the harmonic, sharp, or flat? If it's sharp, how much sharp according to the lights on your tuner?

Does your tuner have variable pitch, so you can tell us what A would have to be set to to show the fretted string at the 5th fret, and the fretted string at the 12th fret as being respectively correct? Are all strings the same or is the B worse than the high E, and the low E worse than the A which is worse than the D (I've left out the G which is sometimes wound and sometimes not, on purpose for that very reason).