i just got my electric yesturday, and when i use my electric tuner for instance on the B string, its pointing to the A on the tuner and telling me thats it, and its trying to tune it to be an A, then i have my top two strings in the same tune and the tuner keeps telling me its right. i had this problem before with my acoustic, and it was because by accident i strung it wrong, i used the same string type for two strings. so i restrung it and it was fine, but i checked and this ones strings are all different sizes and how there suppose to be. how do i tune it to make it go with the right tune, without being afraid to take chance and breaking a string
find a guitar tuner online and listen to the notes, get as close as possible by ear, then go back to your electric tuner and see if it made a difference
it may be that your tuner is a piece of **** but just tune your A string then hold the 2nd fret to tune your B string, make sure they sound exactly the same... (i dont know how youve been playing and if you know this or not)
incubus rocks my world
If the tuner is chromatic it should still work ok although you might have to pluck the strings a little hard to get it to hear the note. It might help to slightly mute the strings you aren't plucking to help the tuner pick it up better. Also some tuners just suck and aren't very accurate.
I had this when I first tried to tune my electric, It was because the string was that much out of tune it was closer to another note. I used the pitch pipe on my tuner to tune the string by ear and then the tuner to get it perfect.
If it's reading the G string correctly, then just tune the B string to the 4th fret on the G string (B).

Also as others have mentioned. Lightly hold the other strings so they do not vibrate in Sympathy and confuse the tuner with overtones.