Modified Mustang bridge intonation woes

[misterfinn]

So I just swapped out the neck on my Warmoth Jazzmaster-y Thing and I'm having a devil of a time intonating the low E. Here's the setup:

Warmoth 10/16 compound radius neck (pau ferro on roasted maple if it matters)
Warmoth modified Mustang bridge (to accommodate the compound radius)
Standard tuning
Strings .011 to .052

Measurements on the low (meaning low in pitch) E string:
Relief .008" at the 9th fret
Action at 1st fret .025"
Action at 12th fret .08"

All the strings intonate just fine except that low E. I've got the saddle all the way forward and it's still reading ~40 cents flat at the 12th fret.

I've read through a number of intonation threads but haven't seen anything applicable to my situation. Apologies in advance if my search fu and/or reading comprehension have failed me.

Any pointers?

 

[Cagey]

If you're using your ears, give 'em a rest. Wait until tomorrow to play around with such fine adjustments.

If you're using an electronic tuner, be aware that some of them are sensitive to harmonics, and will return false readings when frequencies are closely related. You could try changing pickups (neck vs. bridge, for instance) and/or backing off the tone control.

 

[SustainerPlayer]

Maybe a bad string. It happens.

 

[misterfinn]

heh. turns out you're both right! backing off the tone control helped - those 1k pots are pretty bright. i was still sharp so i changed out the string and that put me back in the ballpark. thanks, guys.