RockGuitar101

I hate to say this but measure your guitar neck length, find the scales online. And see if yours was built off scale even slightly.
Also hows your hearing? maybe your adjusting it off key?
Also If you trust string tuners they are never perfect.
Learn to adjust your sound of the strings by ear.
Also if your frets are higher than normal around the 12th fret,cheaper guitars are built this way many times,companies figure your never going to play this high anyways.......but...if your frets are too high then your string can be off tune when you press down on the 12th fret. did you know that even on the best guitars, the harder you press down on a string on the fret the more you warp the sound?
try press your low bass E string at the 3rd fret as you would normally, then press it as hard down as you can, the sound will wrap some, this is most noticable on heavier strings, but it happens also on higher strings. If this is what is happening have some one at a shop file down the last fret or 2 . but don't do it yourself. I have been repairing my own guitars for years and building guitars. This is a common problem.