Intonation quest

Just curious, what are you getting pitch-wise elsewhere on the fretboard on the high e string? 11th fret, 5th fret, etc.

Now this is weird...in a good way.
Checked it for intonation on the high E again...12th fret right on E. It came up F for a week and now it's E.
13th fret is a bit high.
Tuning on other frets is almost right on.

I can take care of the high fret if I can find a brass hammer.

Thanks guys, not sure what's going on other than some temperature changes. Not drastic. 

Ryder, are you using a clip-on tuner?  If so, what you describe is more common than many players realize.  

It's due to how these little tuners sense vibrations through their spring clips, and everything in the universe has at least one resonant frequency.  This means that where on the headstock you clip a tuner can either reduce or improve its ability to correctly sense the note you've struck on the instrument.

Next time you run into this issue, move the tuner to a new location on the headstock and try again.   Sometimes moving it as little as a half inch in either direction makes a big difference.

If you're using a pedal tuner and you're getting unreliable readings, make sure the battery voltage it up, or make sure the power supply is able to deliver the voltage/current the pedal requires for proper operation.

Certainly try it with the one spot all on it's own so no other pedals are drawing current and see if you get noticeably different readings. If not, that's almost certainly not your issue.

Well, only using the tuner on the one spot did the trick.
No problems and perfect intonation! Wow, I'll certainly remember that one.
Thanks you guys!

Ok so there's a weird physics things that happens that is nothing to do with tuners and headstocks or voltage/current that may be relevant to Henry J here...

The low E string will often sound sharp even though it measures correct or even slightly flat. This is noticeable when we play a note on the low string and compare it to a note on a higher string. It drives me craziest when comparing low E string to G string.

e.g. Place a capo on the 9th fret. Tune the G string as perfectly as you can. Fret the low E string at the 12th fret and tune that note as perfectly as possible. Compare by ear the low E string 12th fret and capo'd G string 9th fret. The low E can sound obviously sharp while the tuner reads correct or even slightly flat. That's because the tuner is measuring the fundamental tone of the note, but stiffness of the (relatively thick and short) low E string is forcing higher harmonics to be sharper than they should be theoretically. As a result, the string *sounds* sharp to our ears and can sound out of tune even though the tuner reads correctly. This is very common but most people don't notice it too often. That said we all know that a low E string above the 15th fret sounds awful and this is why; the string is now too short and stiff to play in tune with itself. Add single coil pickups with strong AlNiCo5 magnets adjusted too close to the strings and tuning can get truly weird.

The guitar is an imperfect instrument. Even if theoretically perfect fretwork and intonation was possible, real physical strings do not behave perfectly. There are times when we use our ears to get the best tuning compromise we can and live with the results. And remember, just about all recorded music uses guitars with exactly these issues and a lot of that didn't use electronic tuners. It's not as big a deal when playing real music as it seems when we're fiddling with tuners and screwdrivers.