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Is this normal?

Sounds like you've had this for years so I'm assuming many different E strings and same issue. You might try getting a heavy C clamp and clamping on your headstock and see if it changes the overtone/dullness. Usually Fender necks have a goofy spot on the G string that can be remedied by adding or removing weight from the headstock. I had one with dull spots on the neck and switching to super lightweight tuners cured all the dead spots on that particular bass. Maybe it'll work for you E string.

Also ... I assume you've made truss rod changes over the years? Just mentioning that because it's possible the truss rod is just resonating in a certain way and maybe loosening it up and tightening it back up again might reposition it just enough to stop the issue? Wild shot in the dark but sounds like you've already tried all the obvious answers.
Hey never read that advice, thanks!! I did try a fat finger and noticed nothing, but not the truss rod.
 
This thread prompted me to do two things...

1) Check all my basses for this...I had never even really noticed: Sadowsky has a similar (slightly less pronounced) angle on the B string. My Warwick has angles on pretty much all the strings. FBass appears to be dead straight on all strings.
2) I looked up Witness Points, learned about them for the first time in 30 years of playing and stringing basses, and realized the post I was reading and "liked" was from 2012.

How did I miss this? LOL
 
So I just discovered after years that on my Dimension the low E goes at an angle to the right behind the nut. None of my other basses do this, and online pics of other Dimensions don't either. I'm wondering if this is why I've battled with strange overtones and dullness on the low E starting at about the 3rd fret, even after extensive trouble shooting like witness points, pickup height, etc.
View attachment 4549208
That really shouldn't matter. The strings vibrate from the witness points, regardless of the angle they're pitched at. Strange overtones, and dullness sounds like a twisted string.
 
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So I just discovered after years that on my Dimension the low E goes at an angle to the right behind the nut. None of my other basses do this, and online pics of other Dimensions don't either. I'm wondering if this is why I've battled with strange overtones and dullness on the low E starting at about the 3rd fret, even after extensive trouble shooting like witness points, pickup height, etc.
View attachment 4549208
You ever look at the funky angles of ibanez headstocks?

Zoom in on any Ibanez bass. Especially the 5 strings. And they all have no issues.