strange intonation issues

Have you tried changing the problem string?

Intonation problems are often the main sign the strings are old and need changing.

When was the last time you changed strings?

brand new strings changed 4 days ago when i got my new boss gt-10...it doesent matter new or old the intonation on the low e stays the same...but as i sleep last night something came to me and i think its being caused by the 13th fret being a little to high im not geting fret buzz or a flat sounding 12 fret note...im not sure though and dont wana be filing on the fret bar untill i get some more ideas....this problem with this string has gone on for sometime now like i said new or old strings it dont matter...thanks for the help

Are you sure that the saddle is actually moving when you turn the adjustment screw? The screw could be stripped and the saddle might not be moving.

There have been cases where the saddle won't adjust back far enough (possibly from a misplaced bridge) and turning the saddle backwards might help ... but you said it's not changing at all so this might not be the case.

With a high fret I'd think you'd get buzzing. But just take a straight edge and lay it across that one and the nearby frets to see if it's raised higher than the others.

Just throwing out ideas ...

ideas at this point is what i need my friend...its driving me crazy ...so far i have raised the action to almost a point of unplayability and still no change....yes the the saddle moves when turning the screew :) and it doesent seem that the 13th or lower frets are causing it....im thinking ima take the bridge off my ltd and see what that does on the BC~Rich.
do you think shiming the neck on the low e side might change things?

Take the saddle out an flip it around. I can't see your Tune-O-Matic, but will assume that the saddle's ramp (45 degree angle?) is facing toward the bout, and the flat rise is facing forward. Turn it into the opposite configuration, and the saddle will travel back further, to the end if necessary, and the take-off point of the fat E string will also be further back.

Again, though you say the intonating doesn't change, I take the liberty of thinking that the string is too sharp, and remains in the sharp "range" which is perceived as no change. Short strings are sharp. I read from your text that you can't get it flat sounding at the 12th. After removing and reinstalling the saddle "backwards" flatten the string by turning the saddle screw appropriately and moving the saddle back to its furthest point.

It will look like this, but I am only commenting on your issue with the E string and don't suggest that you perform the operation on all. Slacken the string before making any adjustment.

Slejhammer mentioned this already, directly above.

http://en.wikipedia.org/wiki/Tune-o-matic

If the bridge is moving, intonation changes. Well unless the nut is moving in tandem with the bridge. I suppose it's possible your neck has come loose.

How are you determining the intonation is out of whack? Do you have any effects in the chain between you and the amp? Have you tried plugging directly to the tuner? How sensitive is the tuner?

Have you checked the relief?

Is the action at the proper height?

yes ive pretty much did all this ima take a pic of the set up and let you guys see it ...as far as the tunner i am using ...its the tunner in boss gt-10....it works awesomly, my other guitar is set perfectly and the other strings on this guitar are set perfectly but this low e is driving me nuts

If the bridge is moving, intonation changes.

Yes, we have basic laws of physics at work here. I feel like we're missing something....

Can we check a couple of simple things just to be sure we're all on the same page? (No offense intended w/simple questions!)

- You're intonating by tuning the open string, then comparing fretted string at 12th fret w/harmonic at 12th fret?
- The Boss unit is new, right? Are you confident you're using the tuner section correctly?
- How did you tune before the Boss? Do you get different results that way?
- You've looked the E string over for bad windings, flat spots, etc? checked the nut for damage?

this is a pic of my guitar..you can see the sadle at half way or about on the low e string....when i move it in eather direction it fails to change the intonation at all....now the wierd thing i just tryed is putting my ltd bridg on my BC~Rich...
its a wider bridge giving me a little more room to play with and moving the saddle all the way towards the neck brings it very very close to being intonation....wich makes me think now that the place ment of this bridge is off from the factory...im not sure ...i wish i hade the cash to take it in .....im so close to just filling up the bridge bolt hole and redrilling it to move the low e end close to the neck.....

yes my boss is tunning things correctly ..i used to use the tunner on my old digitech rp-50 same results with both tunners allthough the digitech tunes things slightly lower then the boss.....
i am sure im using the tunner right..lol...no ofence taking ..lol...
the strings are getting changed right now and ima put this bridge from my ltd on it and see what happens...

Have you tried a different pickup to tune with or changing the volume or tone control. I have seen the low E on certain guitars "overdrive" the tuner input and make the tuning of that string very unreliable. Have you tried intonating by ear? Try putting the saddle where it looks like it should be. You know the way the saddles make two nice little sets of 3 in a slanting pattern? Put the low E where it looks like it belongs and try the intonation check with your ear. Harmonic on the string over the 12th fret and the 12th fret fretted. Not painfully acurate but should be ballpark.

OK I see you made another post with pics. Looks like you only have one pickup and it looks like a powerful one. You say when all the way in one direction it almost intonates? Would flipping the saddle help or hurt? Visually from the picture though it looks to me that if the A string is intonating then you sould be able to get your E to do so. Hmmm ... Nice guitar by the way! 8) I'm noticing you look to have very heavy strings on there. That could be part of the problem too. String guage affects intonation.
yes my boss is tunning things correctly ..i used to use the tunner on my old digitech rp-50 same results with both tunners allthough the digitech tunes things slightly lower then the boss.....
Is the new tuner set to 440 HZ?

Have you tried a different pickup to tune with or changing the volume or tone control. I have seen the low E on certain guitars "overdrive" the tuner input and make the tuning of that string very unreliable. Have you tried intonating by ear? Try putting the saddle where it looks like it should be. You know the way the saddles make two nice little sets of 3 in a slanting pattern? Put the low E where it looks like it belongs and try the intonation check with your ear. Harmonic on the string over the 12th fret and the 12th fret fretted. Not painfully acurate but should be ballpark.

OK I see you made another post with pics. Looks like you only have one pickup and it looks like a powerful one. You say when all the way in one direction it almost intonates? Would flipping the saddle help or hurt? Visually from the picture though it looks to me that if the A string is intonating then you sould be able to get your E to do so. Hmmm ... Nice guitar by the way! 8) I'm noticing you look to have very heavy strings on there. That could be part of the problem too. String guage affects intonation.
yes my boss is tunning things correctly ..i used to use the tunner on my old digitech rp-50 same results with both tunners allthough the digitech tunes things slightly lower then the boss.....
Is the new tuner set to 440 HZ?
i have tryed by ear to no avail....the string gauge is light 9-42 dean markly blue steel....best and onley strings i use..i love the sound i get from them....and yep just checked the boss its tunning to 440hz :).....ive played this guitar to long and love it to much to junk it now...lol...i gota get this fixed...ill let you know what chaging the bridge and the strings do
here is a full look at my axe the pick up is a dimebag seymore duncan

Great picture.

TR's analysis of the post-pic situation is good, and I agree. The thick strings make it harder, but never impossible.

Now I see your latest post, with full pic and reference to TR's instructions. And you state the strings are 9 - 42's or light.

I was saying till now, slacken your 6th or E, and adjust the saddle all the way to the back, if you can, if the screw isn't stripped. If so, push the saddle back as you turn.

The saddle for that fat E is positioned as I thought, and I say that only because I see so many, that I have to put myself in a 'blindfold' situation based on experience, from the earlier post without a pic.

In light of your most recent attempt, now if you may have to: remove that saddle and turn it around, as in the Wikipedia pic that I posted. It should work for you if you have any threads left to grip and not slip, as you tune that grabber of a string up. 8)

I edit this in now, with your guitar being String Through Body, and the new pic with same priciples & position will apply.