I have a cheap Ibanez IJX121 I bought for teaching guitar lessons that I can leave at my work and not have to use my better guitars. It played fine at first, but now the high E, B and G strings have some really bad intonation problems, high E is the worst, than B and G is a little less off. I adjusted the saddles, extending them as far as they will go without coming off of the screws and it made almost no difference... the notes still go flat, bad enough that is very noticeable without a tuner starting around the 5th fret and noticeably worse higher up on the neck.

From what I understand this can be due to a twisted neck? Just wondering what can be done to attempt to fix this, maybe a truss-rod adjusment?

truss rod yeah - but be carefull about doing yourself

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The strings are pretty old, same stock strings that were on the guitar when I got it new so I will give that a try, though I wasn't aware that old strings could affect the intonation THAT severely.

If that doesn't do the trick, I will try the trust rod, just not sure if I will need to tighten or loosen... the action is pretty much ideal as it is.
Damn, replaced the strings and the intonation is spot on... I was pretty surprised to find that was all it took. The notes around the 12th fret of the high E were practically a whole semitone flat before. Thanks for the advice.
Also, I admit I'm a huge newbie when it comes to setting a guitar up but I though truss rod adjustment, although it can have an affect on intonation, is primarily there for the straightness of the neck. Meaning, don't use the truss rod to adjust action or intonation.