My Acoustic Guitar's Intonation is right in place for the bottom 4 strings, But the Top two are off. Octave is 50 Cents flat in B-string and 1 semi-tone flat in E-string.
I thought it was the Truss Rod, but only the top two strings are out of Intonation. So I thought I'd first get advice from MusSE than getting the fretboard messed up.
I read up other questions in MusSE which said using different Gauge Strings might affect this. The problem is that I don't exactly remember the gauges. G is from a 0.13 Set and Everything else is From another set (Same set) and that Gauge is 0.12, 0.13 or 0.14. Since these numbers don't vary a lot, I'm thinking Gauge is not the problem here.
Will doing anything to the Bridge Saddle be a solution. If yes, What to and How to?
Please Help. The Strings fairly new and I'd prefer to not take them off. Should I do anything to the Bridge Saddle? Or Should I put on all the Strings from the same set as G taking off the old strings? Or Is there a different solution?
Please don't close the question saying it has to be focussed, The only issue I have here is that the top 2 strings are not in right intonation and I'm listing all the observations I've made.
Edit: One common thing answers have suggested is going for a higher gauge at E and B. But I want to let you people know that I'm already at 0.12 to 0.14 Range. Is it plausible to go higher? with a Semitone Flat Octave?
Just in case this might help shape the answer more in context. The place where I am is on a LockDown for COVID-19 right now, So I can only wait or Do something with the existing things.
Edit 2: [Solved, thanks to Tim] Two things (See comments in Tim's answer for more detailed version) -
Truss Rod, It was a Horrible Upbow, So anyone reading this for having a similar problem must check their Truss Rod First
String Height at Peghead/Tuner Post was too high up. Strings by design have to leave the peghead at a point very close to the neck's wood which affects effective length of string.