When i tune my guitar, and all the strings are in tune, my g and high e do not work well together. They sound out of tune but on the pedal it says they are. What is the problem?
G string is ALWAYS the first string to go off when my strings get old.
Just like you mentioned that its not tunned even if the tunner says so.

If your strings are new... follow the link i guess...

Good luck
I say screw tuners man. I just use my ear. I use an octave initially to tune it. Then I play various intervals (typically a third and a fifth) and then fine tune.
Gibson Les Paul Classic Ebony with gold hardware
Fender American Stratocaster 3 color sunburst maple fretboard tortoise shell pickguard
Martin 000-M Auditorium
Mesa Boogie F-50
Maxon OD-9
Dunlop 535Q Wah pedal
do whatever you want. But if the tuner says its tuned...and in reality sounds like crap... there is something wrong and you have to fix it. Tuning it by ear might cover it up so its not too obvious but the problem is till there.