Shaving the saddle down is only going to affect your action. That would help if your 12th fret octave is sharp, but since it's not, you need to take a closer look at the grooves in the saddle and whether it's leaning or not.
The key idea is that somehow the saddle has grooved, leaned or muscled its way into a forward position that effectively shortens the length of the string in question and, in turn, does not provide the correct compensation for an accurate notation when fretting high on the neck.
Having your saddle, and its notches, at the correct position will yield you the correct compensation required for accurate intonation along the neck.
It's really just a matter of you figuring out which situation applies.
The symptoms do not equal a diagnosis in this scenario, but the physical evidence in combination with those symptoms do.
It might help you diagnose this problem if you read up on intonation issues and study the physical state of your guitar in relation to them.
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