Hey, I forgot to mention one thing. After reading a bit more about your problem on the Strat and after going on and on as I did about my Strat, I forgot to mention that it seems that you are working against a bridge that has moved as you are trying to intonate your guitar. The tremolo springs are not holding the bridge steady so the tension from the strings is pulling the bridge up off of the guitar such that you cannot intonate it. If the bridge of the guitar "raises up" from it's normally fixed position as a result of the strings pulling one way and the tremolo springs pulling the other way, the tremolo springs are weak and not able to hold the bridge down to the proper place it should be when trying to intonate. I think I am correct when I say that the end result will be your saddles don't seem to go far enough away from the nut to bring the strings back into pitch.

Let's say that you could intonate a string properly on your guitar. Now, all of a sudden, the length of the string is made shorter (the bridge has moved--"raised up"). The string now is shorter so if you re-tune to the note desired, then play the harmonic at the 12th fret, the harmonic should be sharp, i.e., the string needs to be made longer either by adjustment of the saddle, (you indicate that there is no more adjustment) or by getting the bridge to "lay back down" to where it was originally.

I'm pretty sure I'm correct about this and I hope it helps. Let me know how it goes.

Bobby