Ok at least we know that your using the best way of intonating. It could be a lot of things. The next thing I would question is what kind of tuner are you using to make such a delicate procedure? If it's a real real cheap one, then that could also be your problem. Did you ever get the 12th fret in tune compared to the open note on the problem string? If not it's still possible that the bridge isn't where it should be.
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Cort e205 but the same thing happens when I use the built in tuner on my Korg Pandora PX4D multi effects too.
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Did you ever get it to show it was intonated on your tuner? If not, and your tuner is working properly, then you need to know which way the bridge needs to be moved in order for proper intonation. Let's say for example, your trying to intonate the G string, and you have followed the advise and tuned the open string with a tuner, now you press down at the 12th fret to find that your tuner says it's sharp. Well, your going to adjust the saddle on the G string so that you make the scale length longer, example. . move saddle farther away from nut. Now tune the G open string with the tuner again, and check. If it's still sharp, then repeat the process. If you go so far that it won't adjust anymore and it's still not intonating properly, then you have problems. Either do what others have suggested and turn the saddle around for more travel if you can, or look for you having to move the bridge back some.. Yikes..
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yes all the other strings are intonated but I think the strings are little old they are about 2 or 3 weeks old.