Intonation issues - still flat

Hi, maybe one of you guys will be able to help:

as much as I love my new Schecter, I am still struggling to set it up to my liking (or set it up at all in fact).
On my old Dean I have a Floyd Rose bridge, which is currently locked for good. I had it set up for a long time at a guitar tech, and it’s been a long time since I made any changes to string gauge, so that one did not require too much attention from me, so I never learned how to take care of that on my own.

However with the Schecter things are not that smooth for me - it came with ridiculously high action, horribly unbalanced strings and poor intonation.
Once I changed strings to somewhat usable set (9-80 - still a little too floppy on the low end, I will try some heavier gauge next time) and lowered the action, it became playable - with the neck fortunately not needing any adjustment, at least not that I am aware of, but the curvature is similar to what I am experiencing on my Dean - near straitght with slight relief. So far so good.

But I am stuck trying to intonate it and seem to be unable to do so.
Strings from E to E are almost perfect, B and F# is where trouble begin, with both strings going flat at 12th fret, and no more room to compensate - saddles are as close to the neck as the screws will go, loosening them do not move the saddles forward anymore.
What gives? Are there any solutions?
I hate that I can’t really use powerchords on the low end, as everything goes out of the tune resulting in a sonic mess.

EDIT: Sorry, forgot to mention - it is a Hipshot fixed bridge.

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Sounds to me like you’ve almost made this a shorter scale by having the saddles so far forwards, in other words it is possible to have reasonable intonation across most strings with the saddles that far forwards even though it’s actually not right.

If your guitar is 25 1/2 inch scale ( or what ever ) get a tape, and measure that distance from the nut to where the strings sit on the saddles a set them all back to there. From here you can start the intonation process again

EDIT - make sure all your saddle heights and neck adjustments are done first as this will affect the intonation. Intonation should be done last.

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Sometimes a factory set nut needs attention too. Getting a good tech to look at might be a good investment.

Yes, the neck seems ok for me - there is a slight gap on the 12th fret when I press the string on 1st and last frets, very tiny tough - maybe a piece of paper would fit, but nothing more really.
Saddle heights should be fine - I lowered action because it was absurdly high, but kept in mind the fretboard radius - I guess I will have to play with it some more in the future, but for now it is quite playable.
The intonation tough…

From what I’ve read if the intonation is flat then the saddle needs to go closer to the neck - that’s what I did, moved it from it’s original position closer to the neck, but it’s still between 5-15 cents off. Depends on how much presure I use while fretting, those strings are really soft. Also, I’m not quite sure what should I really use while tuning - on my 6string it does not really matter if I use 12th fret harmonics or open strings, there is not much of a difference between the attack and decayed notes in terms of pitch, not so much for the 8string, where the difference is drastic.

I guess so, the new strings are completely different from the original set it came with (9-80 vs 10-74) so that actually might be it - if the two lowest strings do not quite fit the nut, this would (perhaps?) cause my issues with intonation and tuning stability.
Good point.
Shame I don’t really have any spare change at the moment, I guess I’ll have to wait until paycheck.

That’s true but you need to make your adjustments from the starting position which is the scale length of the guitar. I.E if it is a 25 1/5 inch scale, you need to set the string to that length first, by measuring from the nut ( fret board side) to where the string sits on the saddle. And then adjust from there. So you really need to check the original position first because as I mentioned it is possible to go too far forwards and make a smaller scale length, and get it to intonate ( sorry physics aren’t my speciality).

As long as there’s no/not a lot of fret buzz, and the string doesn’t fret out when bending on the higher frets, that’s good enough if it suits you.

Never set up an 8 string, but the principles are the same.

The open string and the 12th harmonic should be as close as you can get with the best tuner you can get - TC electronics version 2 or above or the Boss TU-3 are plenty good enough for intonation for a non-pro.

One last point, even the finest-crafted instruments are only 99% odd accurate as you go up the fretboard until you reach the octave due to that physics thing again. Sometimes you have to trade off for what’s best for you.

Well, I am using tuner app in a DAW (Gtune in Reaper to be precise).
What I meant is that when you pluck open string, the pitch on attack is higher than in decay (goes up and then settles somewhere).
Now, when using harmonics, the pitch stays the same.
It does not matter which method I use on 6string - the pitch is roughly the same regardless if it is harmonic, on attack, or on decay.
On the 8 string it goes widely up, then goes lower and stays there, but given I mosltly use either tremolo picked notes and/or sustained chords with strong attack… not sure which method should I use while tuning. I need to go up a gauge in strings anyways, maybe this will help.

That’s more or less what I did. But if I went extremely too far then I would just shift a semi-tone, wouldn’t I?

I think the point here is that intonation adjustments should only ever increase the speaking length of the string. The idea is that when you fret a string, you stretch it a little, making it go sharp. So you increase the length just a little bit to compensate. There should be no reason to set the intonated speaking length shorter than the scale length. If that’s where you are, you should reset the intonation to the scale length, and try again, being aware that your saddle adjustments should be toward the tail of the guitar, not the head.

Also, I agree that if the pitch of a string fluctuates wildly after picking, you could probably do better with a higher gauge string. That behavior is an indication of insufficient tension, and will make accurate intonation more difficult.

There’s not that amount of adjustment I wouldn’t think on your guitar, but technically yes IF you didn’t re tune the guitar every time you adjusted.

Basically you are re tuning the string at a slightly different length every time you adjust, so it’s -Adjust, Re Tune - Check Intonation, repeat as necessary.

As per induction, heavier gauge could help here. I use Reaper for the odd bit of recording, but pretty old school when it comes to setting up, and everything really :slightly_smiling_face:

If problems persist, as Thegent says the nut often can be the issue.

Technically true but you have to allow for build quality, neck join, bridge alignment, nut, type of strings etc.