I love my Martin tenor, but I'm getting a bit tired of working on intonation all the time.
Rory, what model Martin do you have?
The reason I ask is that I have an old one: a Handcraft. When I got the horn it was in many, many pieces and had been sitting like that in its case for about 20+ years. Layne Francis at the Horn Shop in Dartmouth restored, and I do mean restored, it for me from the ground up.
The regulation he did on that horn is amazing. It plays in tune like no other tenor I have ever played. It is absolutely effortless. Seriously. That's why I use it as my backup horn, despite its quirky ergonomics. I might not have played the horn in a year, but if I need it because my Mark VI is in trouble (like just happened to me at a show last month), the Martin is a breeze to play with no embouchure calisthenics required.
I have no experience with Martins other than mine, so don't know if this is typical, but it is an amazing horn.
Since Layne did the work on my Handcraft in 2000, I have only had it in the shop once with him, in around 2001, for the most minor adjustments, and for adding a front F key from a YTS 23. The Martin moved across the country (keys secured down like the rest of my horns) and still that sucker still plays like it just came from the shop. It subtones to low Bb beautifully.
So all this pontification (sorry 'bout that ;-)) to ask: Could some of your intonation issues be caused by some regulation issues?