I just bought a used guitar and when I tune it all strings are good except for the low E string, which I seem to be unable to tune to E2, which it is supposed to be. What could be wrong?
Taking a wild swing at this...
If you are using a meter & it can't quite grasp the pitch, there are a couple of things you can try.
Pluck the string with the soft part of your finger gently - fewer bright overtones means more fundamental frequency for the meter to listen to. If you pull the string too hard it will pitch-bend - it will start over-pitch [sharp] & drop down to pitch over a couple of seconds.
Rest your finger gently over the 12th fret & pluck as normal, which will create a perfect octave harmonic & tune to E3.
Do it the old-fashioned way & compare the A string to the E on the 5th fret.
It doesn't matter which octave it recognises, so long as it recognises the pitch itself - as it's almost impossible to be out of tune by that much. An octave under it would be like a slack rubber band & an octave over... well, you'd never get there in one piece.
The low E string of an acoustic guitar can generate multiple harmonics that are almost as strong or occasionally even stronger than the pitch. These harmonics are often easier for the microphone (and internal DSP filters and FFTs) of cheap tuners and tuning apps to pick up than the fundamental pitch frequency. So you end up with a bad or misleading tuning indication.
Better strobe tuners (many available for iPhone and Android devices) won’t have this defect.