Problem Setting intonation on fretless basses

I have two fretless basses (Ibanez SRF706 and Ibanez SDGB1) and I'm having the same issues setting intonation.
I get the neck and string height to where I want it, and when I go to line up the harmonic at half string with the octave of the open string, I have one string that I can't get the note to line up with the harmonic, and it's off by almost half a step. The issue is that I can't move the saddle and close to the pickup because I run out of screw and the saddle just falls off. I'm trying to get my action nice and low, and since I'm having the issue on two basses, I have to assume it's something that I'm doing wrong. The other strings work perfectly, but on the SDGB1, for instance, the B string is playing a B-flat when I press down, and I have to slide up quite a bit higher than the other strings to get it to be in tune.

Any tips you might have will be greatly appreciated.

The steps I take for setup are:
1. new strings
2. set string height for outer two strings at end of neck, then adjust the other strings with a radius gauge.
3. set neck relief.
4. adjust string height if necessary
5. set intonation
 
Are you saying that if you play a harmonic at half the open string length, it's not the octave of the open string? How is that even possible? Unless part of your string is dramatically thicker than the rest, the octave harmonic is at one-half the open string length.
 
Are you saying that if you play a harmonic at half the open string length, it's not the octave of the open string? How is that even possible? Unless part of your string is dramatically thicker than the rest, the octave harmonic is at one-half the open string length.
The harmonic is, of course, the octave, the note under the harmonic (when I press down on the string) is a sharp Major 7th.
 
You said the screw is “backing out” and the saddle isn’t moving? You need to loosen the string and/or physically push the saddle forward to move it closer to the neck. Best practice is to always loosen the string when you adjust the saddles in any direction.

As far as the intonation issue, have you set witness points? That can have a huge effect on intonation especially on the thicker strings. Search witness points in this forum, there’s a few good threads. If that is already done or doesn’t help check the nut and bridge saddle and make sure the string is taking off from the very front edge of each.
 
You said the screw is “backing out” and the saddle isn’t moving? You need to loosen the string and/or physically push the saddle forward to move it closer to the neck. Best practice is to always loosen the string when you adjust the saddles in any direction.

As far as the intonation issue, have you set witness points? That can have a huge effect on intonation especially on the thicker strings. Search witness points in this forum, there’s a few good threads. If that is already done or doesn’t help check the nut and bridge saddle and make sure the string is taking off from the very front edge of each.
actually, i said "So the screw is "backing out" even though it's not moving." I was using that example of turning the screw "lefty loosey" which would be the same as backing out the screw, but it's not actually backing out.
 
Have you set the "witness points"of the strings?
witness points 2.jpeg
witness points 4.jpeg
 
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actually, i said "So the screw is "backing out" even though it's not moving." I was using that example of turning the screw "lefty loosey" which would be the same as backing out the screw, but it's not actually backing out.


Ok, I misunderstood what you wrote. I apologize. How about the witness points and break points on the strings?
 
It sounds like that string is damaged , I had the same problem with a Warwick flatwound E string . You tune the string in open E and every fretted note was off a half step . Replace the single string , that should solve the problem .
 
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I often am asked to put side dots/ position markers on string basses. How I do this, might help you.
I use an online fret position calculator- Stew-Mac has one. I'll type in the scale length. Most often, it's 41" or 41.5"
I get the fret positions, and mark the location of the pertinent positions with a sharp pencil. I'll draw a long straight intersecting line, with a straight edge, at half the fingerboard thickness. At the point where these intersect, I use a small punch to make an indentation for where to drill. If you do this, but are not adding any markers- all you need to do to find your octave- is literally capo the point only where the 12th. fret would be.
 
Today I learned that I set witness points without meaning to, and without knowing there was a term for it.

I did it because it looked and felt right. Someone many years ago set up my previous set of strings, roundwounds, correctly, so I took the way they were installed as an example.

The only tip I have on adjusting intonation is, "keep trying." At least for me, doing it the first time ever, I needed a good couple of hours to fully sort it out.

This was with a new set of flatwounds on my 4-string Fender P-bass). I quickly discovered that adjusting the bridge length for nominal scale length (34" in my case), per Fender instructions, only got me in the ballpark. Lots of fine-tuning and re-tuning ensued. I ended up with something greater than 34" of free string length on E, before all the notes above fret #12 were finally dialed in.

Maybe I'm still doing it wrong - TBD. Seems to be working for me so far.

If Ibanez has standardized instructions for bass setup, it might help to go through the steps. I don't doubt that OP knows what he's doing, but sometimes it can be helpful to have a "reset" by referring back to a standardized procedure.

If that still doesn't help, then I'm stumped.
 
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