Hi all
I have a Fender Stratocaster standard tuned in Eb (one haltone down),
and I have the following tuning problem:

I tune correctly the G string but then if I play A (on that string) it sounds not tuned,
if I tune correctly that note then the G string played empty sounds not-tuned...
The same happens on the B string...
I cannot tune those strings so that each played note is well tuned... everytime I have to retune those strings according to the song I'm gonna play and choose to have it tuned when played empty or tuned when played the other notes...

any suggestion?
Sounds like you might need your intonation checked. That is the adjusting of the bridge saddles forward or backward so that fretted notes play in tune.