adjust your intonation. its influenced when you
1. adjust saddles
2. adjust necks - may i know why are u risking your whole guitar doing this
3. adjust string height

if you've set your intonation before, its normal for it to go slightly off if you've been using your strings for many months.

another tip when tuning.
1. dont just press anywhere within the fret but press right behind the fret. that will give the best accuracy.
2. when tuning with a tuner, its better to pluck the chord with your thumb than with a pick as you dont want additional harmonics to confuse the tuner.