Something I just learned lately. When you pick the string you are tuning, do you pluck the string as hard as when you actually play? It's surprising how much the difference is. Take that low E string when tuning and change the pick attack and watch the pitch change. The harder you pick, the sharper it goes.

I wouldn't have believed it if I hadn't seen it myself.
Same with the G string. Something weird about the physics of the instrument.

There's a video on youtube about this. Long, 50 min. on tuning.

Just something to check.....