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Question about an issue I am having with intonation.

Sometimes a bass will intonate on the fundamental but the low order harmonics sound out of tune. By that I mean the parts of the note that we often identify as the note actually sound out of tune. Usually that’s because the pickups might be pulling too much on the string, the string is twisted, or there might be a flaw in the string. I’d try adjusting the pickups so they are farther from the string and see how that sounds, and/or changing to a different string type or brand.
 
I guess correct string spacing isn't included in Sweetwater's 55 point inspection... How can they (or Fender) ship out bass like that??? That's absolutely shocking. If that's the best they can do, it would probably be better if they just moved the boxes in and out of the warehouse without ever opening them.

When they ship out a bass like that, there could be a number of other issues with the setup too.

Poor intonation could be caused by a number of things:

-Pickups too close to the strings can mess with the tuner readings.
-Intonation that's WAY off can sometimes make a tuner read it as correct.
-Too much neck relief, too high nut slots or too high saddles can affect the intonation.
-Poorly set witness points can also mess with the intonation.

I would start by checking all of these things.

Faulty (including damaged/twisted) strings seem like a very unlikely cause in this case, because there's practically no chance that all strings on a brand new bass would arrive faulty.

Based on the pic, the saddles look like they are more or less in the correct positions (at least relative to each other) although I would perhaps have expected the E-string to be slightly further back vs the A-string. Then again, it's impossible to say anything for certain based on a pic.

This is probably something that's very easily fixed, but it's impossible to give any definitive answers without actually inspecting the bass.
 
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Is the bridge placed correctly? If it's not in the right spot it will never intonate correctly, anywhere. Fret placement on the neck is all mathematically divided and if it's not intonated properly at the 12th, it will throw off the intonation all over the neck... even below the 12th fret.

Pickup height can make a difference too as others have mentioned, but if everything 'mechanically' is right with the bass, then I too suspect a bad string (or entire set of strings). I had one string going bad in a set once and I could not get it to intonate for the life of me. It broke not long after installation, so it was unstable the whole time.
 
I had Sweetwater set up my bass before shipping it to me and it seems like they did a decent job.
They most definitely did not. Look at that string spacing! Seriously, if they actually set up the bass for you like that... that's just shocking.

Of course, the string spacing won't affect the intonation, but if they mess up something as glaringly obvious as that, who knows what else they've messed up.
 
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They most definitely did not. Look at that string spacing! Seriously, if they actually set up the bass for you like that... that's just shocking.

Of course, the string spacing won't affect the intonation, but if they mess up something as glaringly obvious as that, who knows what else they've messed up.
In 2014 my Am Standard arrived from SW with the same problem. Thank God for 3-groove saddles.
 
In 2014 my Am Standard arrived from SW with the same problem. Thank God for 3-groove saddles.
Well yes... and no.

The thing is, if the instrument is properly made there shouldn't be any need for 3-groove saddles. Only ONE of the saddle grooves can ever be the correct one, and a single, centered string groove on each saddle SHOULD line up perfectly on a properly made instrument. Fender's 3-groove saddle really just allows you to mess up the string spacing in two different ways (on each saddle...). The grooves on the 3-groove Fender saddles are so far apart that two of them will always be VERY misaligned. I've never understood why Fender use these saddles to be honest, unless it's a sort-of compensation for sloppy manufacturing/QC...???

Assuming your AmStandard is properly made (and I think we can assume that it is, the AmStandards were generally VERY good basses) it probably wouldn't have arrived with this problem if it had "standard" saddles rather than the 3-groove saddles. So basically, the 3-groove saddles really just allowed you to fix a problem that was caused by the 3-groove saddles in the first place...;)
 
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