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D string intonation went wonky

A few days ago, I pickup my bass and start playing only to notice it was sounding a bit off. Check tuning, check intonation and sure enough, the intonation on the D string was completely off, but I mean completely off. To get it to intonate properly the adjustment is now completely at the end of its travel(there's only like 3 or 4 threads left), as before it was about midway(where the other strings are).
I checked the string(Fender 9050L) with a magnifying glass, looks fine, no apparent damage. It sit properly on the bridge, it is properly under the string tree, the nut is fine, and it otherwise sound fine.
That is bizarre, I've never heard or read about such a thing.
As this happened to you, and have you found the culprit?
 
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If not the string, I'd suspect something happened at the nut...maybe the bridge...which altered the contact (witness) points. I would remove the string inspect the slot...file / smooth as necessary...replace the string, tune-to-pitch and re-set the witness points at the slot and bridge. This should have been done during the initial install.

Could be the string but we're ruling-out the simple stuff.

Riis
 
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If not the string, I'd suspect something happened at the nut...maybe the bridge...which altered the contact (witness) points. I would remove the string inspect the slot...file / smooth as necessary...replace the string, tune-to-pitch and re-set the witness points at the slot and bridge. This should have been done during the initial install.

Could be the string but we're ruling-out the simple stuff.

Riis
The nut is a custom bone job done by Montreal guitars, the premier Fender service guy in North America, about 1 1/2 year ago. Nevertheless, I just did remove the strings, but there's nothing wrong at the nut, no cracks or apparent damage and the strings keyway are astoundingly beautifully made and polished.

Checked everything at the bridge again, it is one of them quick strings change one, nothing seems amiss. put the strings back one, they all intonate perfectly, including the D except for the fact that it's about 3/8" to 1/2" further up the adjustment screw than it was last week and for the last 1 1/2 year.

Wish I had another D string to try on but I don't(well, I do, but a different type, make and model).
 
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Can you post a pic of the bridge so we can see how the saddles are positioned?
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1000008161.jpg
 
It is kind of unusual the way the D saddle sits so far up. The part I don't understand is the D was intonated fine the last time you played it, then all of a sudden it's out that much today. How long between the time the D was fine and it got all wacky?
Hard to say exactly, intonation problems do not show up until you play higher up the neck and I'm not that kind of player, but couldn't have been more than a few days.
It doesn't currently hinder my playing in any way, it sounds fine, and as it stand the intonation is also fine, it's just a very bizarre thing that got me very curious.
 
The nut is a custom bone job done by Montreal guitars, the premier Fender service guy in North America, about 1 1/2 year ago. Nevertheless, I just did remove the strings, but there's nothing wrong at the nut, no cracks or apparent damage and the strings keyway are astoundingly beautifully made and polished.

Checked everything at the bridge again, it is one of them quick strings change one, nothing seems amiss. put the strings back one, they all intonate perfectly, including the D except for the fact that it's about 3/8" to 1/2" further up the adjustment screw than it was last week and for the last 1 1/2 year.

Wish I had another D string to try on but I don't(well, I do, but a different type, make and model).

Big thumbs-up on the bone nut...mine are unbleached so you don't see that glaring white juxtaposition against the FB. Can't explain the sudden intonation disjoint as, per your description, nothing has changed or been altered. I hate gremlins. I'll assume everything is in tune fret-by-fret?

Riis
 
I had something similar happen with Ernie Ball Slinky Cobalt Flatwounds, except it happened on a brand new set of strings -- actually two new sets. I strung up my bass and the G string would not intonate. I knew right away it had to be a bad string, so I pulled the G string out of another set of those strings that I had in my inventory. Same thing. So I thought it had to be some flaw with the bass, which was a brand-new-to-me used bass. I took it to my luthier. After checking it out, he said it was indeed the string. Those two sets were purchased from two different vendors six months apart, but he was right, it was the strings. Nothing looked to be wrong with either of them. I contacted Ernie Ball CS and they sent me two new G strings, no charge. I had no problem with those two. I have no idea how Fender might handle that, but I'd try contacting them.
 
I had something similar happen with Ernie Ball Slinky Cobalt Flatwounds, except it happened on a brand new set of strings -- actually two new sets. I strung up my bass and the G string would not intonate. I knew right away it had to be a bad string, so I pulled the G string out of another set of those strings that I had in my inventory. Same thing. So I thought it had to be some flaw with the bass, which was a brand-new-to-me used bass. I took it to my luthier. After checking it out, he said it was indeed the string. Those two sets were purchased from two different vendors six months apart, but he was right, it was the strings. Nothing looked to be wrong with either of them. I contacted Ernie Ball CS and they sent me two new G strings, no charge. I had no problem with those two. I have no idea how Fender might handle that, but I'd try contacting them.
It's one thing to have a bad string out of a brand new package; it's quite another for the intonation on one string to go wonky after one and a half years of being played.
 
It's one thing to have a bad string out of a brand new package; it's quite another for the intonation on one string to go wonky after one and a half years of being played.
True, but unless you see any damage to the bridge or the tuners or the nut or the bass itself, what else can it be? Strings can go bad any time, though thankfully it happens very seldom. Try temporarily putting another string on it. It doesn't have to be a match to that set, just any other D string. This is just a test, so even a used one would do. See if it will intonate properly. If it does, you have your answer. If it doesn't, keep searching.
 
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I had something similar happen with Ernie Ball Slinky Cobalt Flatwounds, except it happened on a brand new set of strings -- actually two new sets. I strung up my bass and the G string would not intonate. I knew right away it had to be a bad string, so I pulled the G string out of another set of those strings that I had in my inventory. Same thing. So I thought it had to be some flaw with the bass, which was a brand-new-to-me used bass. I took it to my luthier. After checking it out, he said it was indeed the string. Those two sets were purchased from two different vendors six months apart, but he was right, it was the strings. Nothing looked to be wrong with either of them. I contacted Ernie Ball CS and they sent me two new G strings, no charge. I had no problem with those two. I have no idea how Fender might handle that, but I'd try contacting them.
Well, at the very least I now know that something in the string itself can affect intonation drastically. I was starting to doubt myself... I mean, I figured a string is a string is a string, but there could be more to it.