It could be minor issues with intonation.
I get that too sometime, mainly with my Gibsons.
Sometimes the guitars sound spot on after tuning.
Other times, just a minor tweak on the high E or B or rarely the F strings, needed to get the D or A to sound proper.
I think its a combination of humidity as well as accidentally hitting it spot on with the tuner.
I'm talking less than a 1 cent tweak that brings everything into harmony.
Probably a finer resolution than the tuner can pick up but maybe not your ear.
God bless the good ear !
Harmonics101