Intonation out on A string of 1966 Martin D-18

Hello

I'm a first time poster to this forum, but have read it and Frank's blog for awhile now.

I have a question that seems like it could be addressed by you fine folks. I have a 1966 Martin D-18 that has had alot of work done to it. That I know of: the neck has been reset at least once, the bridge has been moved (if not replaced), the saddle has been shaved, and the frets have been dressed. When I got it the A string was extremely flat past the third fret. I changed to 3 different string brands thinking that the strings were the culprit. Not the case, all of the other 5 strings tuned up and intonated just fine all the way up past the 14th fret, but the A string was still bad. The first 3 frets are golden, and I can play cowboy chords all day long, but as soon as I move up past the 3rd fret it all gets shot.

I took the guitar to a repairman who said the bridge was in the wrong spot. He made the proper measurements and moved the bridge and still found the A to be flat and exhibit the same symptoms as before. He then built a "shelf" to try and accommodate for the flatness at the bridge. This helped a little bit, but I still can't play it past about the 4th or 5th fret depending on the chord I use.

So, I ask you guys. What could be the culprit? Has anyone dealt with anything like this before?

Here are a few pics for reference: