I have this problem on two different guitars, one a lap steel and an acoustic. They will fret true with 9 or 10 strings but with heavier strings will not. They will tune up fine with my electronic tuner but will not fret true. I should add that the acoustic has had the nut and bridge raised to use as lap steel. I have checked the scale on the acoustic, measuring from nut to center of 12th fret and doubling which is 25". Any suggestions?
Changing the gauge of your strings can require an intonation adjustment to get everything playing true again.
http://www.projectguitar.com/tut/intonate.htm
http://www.guitarattack.com/repair/intonation.htm
http://www.frets.com/FRETSPages/Musician/Guitar/Setup/Saddle/saddle01.html
Depending on the type of bridge you have, it can be fairly easy, or require some effort.
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Thanks kent-eh, I appreciate the help.