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I keep trying to intonate my MKII project so I can paint it. I've measured the scale, and calculated the bridge position about 10 times now, and when I try to tune on the 12th fret, it's always noticeably sharp, and no amount of saddle adjustment will fix this. It does however intonate on the 11th fret. Does this have anything to do with the zero fret? What am I doing wrong? Thank you

I will be waiting to hear some info on this one !
Intonation is always somewhat touchy and the zero nut is something I'm not familiar with!

to be sure it is or not the nut
put a capo in first case and try yo intonate at 13 fret
for intonation on my build i put always +6 mm on e bass and 3 mm on e treble in general then i try to place the bridge always a little more than the scale lenght to avoid to have the saddle push too far
but it depend of string gauge for sure i use 10 52 and also of the hight of the string on the fretboard too hight string more need to push the saddle

make sure that the string guide sits lower then the zero fret. remember the zero fret on a mosrite is the actual nut and if the string guide sits higher then it, then the nut will start at the string guide and in turn throw off your entire neck.

This may be a stupid question, but are you counting the zero fret as number one ? I can't imagine being an entire fret off for intonation, unless a major mistake in the scale length has occurred.
Also keep in mind that you measure the scale from the zero fret, not the nut.
Dan

I know Ed Roman is not the man of the year here, but I read an article that I gleaned one important item from that has helped me on every setup so far. Double the scale to the 12th fret and add 1/8" for mid line saddle position.
Dan

Yes you need to add at least 1/8" to the length for compensation. It really depends on the type of bridge you are using.

Bob

I recently built a guitar, and after much the same problems, discovered I had counted my markers wrong!!! When I counted right, it intonated perfectly Gonna hafta put a new fretboard on that one one of these days!

mick told me it was the string guide like I suggested. appearently it's been fixed now.

Could you elaborate on the String guide, How does that effect intonation.
Dan