hi, i have a fender squire strat

I little while ago i noticed that the intonation on the highest E string was about half a semitone off, and my teacher told me to adjust the length of the string on the bridge.  I tried making the string shorter, but i ket turning the screw and it only helped a little bit.  Eventually the screw went as far as it would go and the 12th fretted octave was still flat.   I heard that i might have a problem with the neck warping?  Anyway, is there anything I can do to fix it? or is it time for a new guitar (this one was cheap-only $150ish).  Also, last week this started to happen with the B string, but not as bad.

thanks for any info guys.

Just a thought..... yea... try a new guitar, but yea, it sounds like it may be warped. Adjusting the neck may help, but I would have to see it to be sure.

I dont know what size strings you have but going up one size helps, I went from size 9s to 10s and it helped alot just a thought.
Keith.