Alright so my schecter hellraiser has a problem with the first string, the higher you go up the more flat bad sounding the notes get to be...its about a whole half step down at the 12th fret. I tried adjusting the intonation at the bridge but that doesn't change anything..am I doing something wrong?
Keep adjusting it.
Yea, I've had this problem before, where you keep adjusting the bridge but the intonation stays out. I have this problem on one of my basses where the low E string can't be adjusted any further bit it's still out. Sometimes it just happens and either live with it, or get a tech to work some magic on it.
Tune at headstock, check int, tune int, retune at headstock, check int, tune int. rinse and repeat untill you get a nice golden sound.