This came to mind. If it is only the A string, you do have a Fender designed bass. As John says thereās a flaw in the design. Easy to test, press down on the A string about an inch behind the nut, hold it down and pluck with your other hand. It should sound steady
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Does āshouldā sound steady mean that it should sound steady if there IS a design flaw or if there is NOT a design flaw? And, for that matter, what does āsound steadyā mean?
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It means the note should be consistent with no wavering or chorusing effect. If it holds steady, you have the flaw and it can be remedied by winding new strings as low on the tuner post as you can get to help the angle of the strings.
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This is interesting, can you post a short video? I know that if the core wire is broken then it would sound dead. Similar things happened to me a few times but they are from different problem. One was from an improperly cut nut.
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The design flaw is not in question - all standard Fender style headstocks are susceptible 
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Hi @beecherscoville, good to have you! Say hello here, if you like 
I think you have all the tips you need - my first step would be to check how well the string sits on the tuner peg, as has been mentioned beforehand. Have a look at this video by Fender.
If you got a setup, perhaps call and ask about this. My local music shop has a great technician, so perhaps you can get recommendations to find one around you.
Cheers,
Antonio
Really good video, easy to follow.
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This is a strange and interesting issue.
I think that if I was to try and really diagnose it, I would need a video of two things simultaneously -
You playing the bass, fret by fret, on the suspicious A string while also seeing your tuner as you move up the neck, to see what it is registering.
My first thought is - wonky tuner.
My second thought is - because it comes and goes - left hand shenanigans, pressure, bends, or other inconsistencies while fretting.
My third thought would align with what the other folks said with intonation or possible gear issues.
I wouldnāt be able to back up any of these suggestions unless I could see and hear what is going on.
Hope something in this thread helps solve your mysterious mystery.
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Iām glad that, as usual, thereās a lot of helpful responses in this thread. Iām just a bit sad that nobody took the chance for a string theory joke 
goes back hiding in the corner
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Well, this was my very subtle and subdued attempt at one:
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Iām sorry Iāve missed it, the useful comment after it distracted me. Itās also pretty subtle but mean, I like it 
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Very true - but the thing that makes me think āFender A string deisgn issue and how the string is strung on the tunerā isā¦
- its a Fender product (Squier Affinity)
- its the A string
- it has bit me in the arse more than once
- it can act like a wonky tuner
After that, I am suspecting the nut.
- I just had this issue on the E string of my Squier Bass VI with the crappiest of soft plastic nuts they give you, a little crazy glue / powder reinforcement did the trick.
- Since this is an Affinity series, could be same crappy nut issue
I might have missed it but I donāt think @beecherscoville has commented on if he changed the original strings or not, which would be my #3 guess, or maybe number 2.
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Sticky nuts do happen. I canāt believe I just typed that.
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Well, itās not a wonky tuner, seeing as I neither need nor ever use a tuner to hear elementary intervals ā in this case, fourths, thirds, and half-tones.
The issue comes and goes, so Iām not sure that I can post a video that would be of any help. I have, though, attached, a shot of the nut, which was mentioned above as a potential culprit. The guy who did the very quick, dirty, and cheap set up told me that nuts are very cheap if I wanted to buy one and start afresh at filing it down myself, which to me suggests a lack of complete faith in his own filing of the nut.
In any case I am going to change the strings which will hopefully take care of things (and yes, the string theory reference was too subtle for me to understand what was āmeanā about it).
Up next, need to figure out what kind/size of tool I need to order from Amazon to adjust the neck truss on my even more recently purchased Glarry fretless.
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I went to Harbor Freight and bought a set of Allen wrenches. One will be the right size for the truss.
Others will be the right size for adjusting bridge saddles.
See how the A string has very little to no break angle once the nut compared to the others.
Bad news.
You should have 2-3 windings on all pegs, but that Fender A the more windings the merrier to keep the string pushed down the peg. Itās sitting way too high.
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Thanks for your experienced eye, John. In the only re-stringing I ever did (putting flat-wounds on my fretless) I followed Scottās advice of leaving about two extra tuning peg spacings of string, but looks like Iāll need more here, at least for the A-string. How much extra string do you leave for winding purposes?
3-4 wraps at least. More wonāt hurt you as long as they are near on the peg. 4ā will probably only get you 2 winds. See if you can get the whole uncut string on.
It means that the physics explaining metal string vibrations is well know and not in doubt whatsoever. The theory concerning another kind of string, however, is (are? There may be competing ones, iirc, a bit like conspiracy theories) not so solidā¦ 
Hopefully now we can go back to bass, or condiments 
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I have an astrophysicist friend withā¦ stories.
Iām fine with the theories as long as they donāt call them science. More like one currently orthodox astrophysics religion. To be science, well, first they need to follow the scientific method.
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