Saddle height doesn't really play much of a part in setting intonation, it's mainly to adjust the action, sure, adjusting saddle height on a already correctly intonated guitar will knock it out by a cent or two but if your intonation is that far out that you can't adjust it with the fore and aft movement of the saddles then your problems may lie elsewhere, (bridge, neck relief etc)

What kind of guitar is it? some bridge/saddle designs don't allow for 'perfect' intonation i.e Telecasters with 3 saddle bridges.

If the guitar has always had this problem then it could be a build issue, bridge mounted marginally too far forwards or backwards on the body for example.