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Help needed badly.

Are you familiar with the "twisted string" theory? I assume you put all the strings on so it could be your technique. The theory being if you wrap your string around the post vice pulling it around the post by turning the key (and don't allow the other end to turn freely) the string could be torsionally loaded and its performance affected. If you take it off the post completely and let go of it and it should stay aligned in its position. If it untwists - "thats" what they're talking bout.
 
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These aren't the greastest pictures.
 

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Are you familiar with the "twisted string" theory? I assume you put all the strings on so it could be your technique. The theory being if you wrap your string around the post vice pulling it around the post by turning the key (and don't allow the other end to turn freely) the string could be torsionally loaded and its performance affected. If you take it off the post completely and let go of it and it should stay aligned in its position. If it untwists - "thats" what they're talking bout.
I tried seating the ball first and then wind. This last time I let the ball work it's way into the bridge so that if the string does want to twist it can do so freely. Not sure if I'm making any sense.
 
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What kind of bass is this? I'm not familiar with this bridge (they're all about the same though)
Looking at the end. 3 of the string eyelets fit in there at an angle. The D string looks different. I'd investigate - could be nothing.
Looking at the other end - saddles are very low (not good or bad.... depends).
Do all strings play a clean note all the way up the length of the board?
Notice that the D string is at the end of travel of the screws. Then notice that they don't all look to be the same lengths. I'd probably shift them all around Longest on G and tapering to the E which is typically the shortest. What does this have to do with it... dunno... probably nothing.... but my OCD couldn't leave it like that. hahahaha
Your saddles appear to be way out (long) - fine, it is what it is.... look at the springs, are they sliding around or are they held in place by their spring length/tension. They shouldn't move really?
 
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Beyond the nut slot shape, back notch and depth, bridge saddle and slot , the tuner itself and anything structural or the frets themselves nothing really lends to going flat. Usually it all goes sharp. Assuming it was stretched but even then this problem is odd. I think you will eventually ferret it out. Best of luck!
 
This is a strange one but it still sounds like a bad or twisted string. (happened to me with a set of Ernie Ball flats one time years ago and freaked me out...) Coincidentally it was the D.

Not to rule anything out, but I seriously doubt fretwear is causing one string in a new set to register flat notes.

I'm curious, how flat does your Peterson say it is? Are we talking a couple cents or waaaaay out. Because waaaaay out before the fifth fret is an obvious problem.

That it’s only that D string kinda' nulls this, but you could be getting some pickup phasing. Like if that string is really close to one, but further away from another. I had this happen on a Strat I was setting up one time. Couldn't get the top-string to intonate.
 
When I played the E string on the frets close to and including the octave on my 4-string Gibson EB bass (from around 2011; the short-lived model with two big humbuckers), it made a weird chorusing sound through amps.

I tried a few fixes and then thought to try dropping the height of the neck humbucker. I gradually brought it down from the original height of a little over 1/4", checking after every incremental change to see if the problem was still there. It wasn't until the neck pickup was nearly flush with the pickguard that the chorusing went away.

Dropping the pickup barely affected the output of the strings, but it got rid of the warbling chorus sound.

Different problem, but it might be worth experimenting with pickup height. And maybe with string gauge or material, either of which might affect the interaction of the D string with the pickup(s).

Edit: checked back through some of your posts to take a look at what basses you own and saw that you were considering buying a Musicman Stingray a while back. If that's the bass you're having the problem with, I'd suspect the pickup or its height, if only because the pickups on my EB bass look identical to the Stingray pickup.
 
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This sounds like a bad string, as was mentioned before.

If your set came with a bad string, the string got replaced, and is also bad, there might be something causing that.
That something might be on the bass guitar or it might be user error.

I would inspect everything that touches the D string, and look at the old string for potential damage. I see in the background of the headstock pic that some silk has accumulated at the string tree - is the string okay in that area? Are there sharp edges at the string tree?
Is the nut alright?

As I said, check everything that has direct contact with the string.
 
These aren't the greastest pictures.
I have no certainty around this, but in that 3rd shot I could convince myself that the D string is being pulled out of alignment by the pickup being too close to it. The D appears to me to be angling down toward the body going away from the bridge in a way that the others are not.
 
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What kind of bass is this? I'm not familiar with this bridge (they're all about the same though)
Looking at the end. 3 of the string eyelets fit in there at an angle. The D string looks different. I'd investigate - could be nothing.
Looking at the other end - saddles are very low (not good or bad.... depends).
Do all strings play a clean note all the way up the length of the board?
Notice that the D string is at the end of travel of the screws. Then notice that they don't all look to be the same lengths. I'd probably shift them all around Longest on G and tapering to the E which is typically the shortest. What does this have to do with it... dunno... probably nothing.... but my OCD couldn't leave it like that. hahahaha
Your saddles appear to be way out (long) - fine, it is what it is.... look at the springs, are they sliding around or are they held in place by their spring length/tension. They shouldn't move really?
It's a 2013 Fender American Standard Precision. I'll check the eyelet on the D and see what I can. The rest of the strings have no issues. It's just the D.
 

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