One of the most difficult things for a sax repairman to do is a proper setup. Anyone can change the corks and springs, and put new pads on a horn. There are very few sax technicians who really know what they're doing when it comes to regulating the key heights. Each horn needs to be regulated differently in order to play in tune. Often classical guys like a lower setup than Jazz players. As you raise the key heights the horn becomes more free blowing, but the intonation gets wilder. The trick is to open the keys up just high enough to get the maximum sound possible, without messing up the intonation. It's a very fine line. Personally, I like higher than normal key heights. This has opened a Pandora's box of intonation problems.
When I first got my current Mark VI alto I discovered an annoying gurgle on the high C. It sounded like there was a lot of spit in my mouthpiece. The rest of the horn played great, except that one pathetic note. I learned that this is a common problem on Mark VIs. The only effective way to eliminate the gurgle is to raise the upper stack enough that it goes away. On my horn the keys ended up pretty high. This threw out the intonation because now the palm keys were different in relation to the upper stack.
I only know a few techs who I think are good enough to setup difficult horns and get them to play perfectly in tune. One of these guys is Randy Jones of Tenor Madness. When Randy sets up a horn he uses a strobe tuner to make sure all the partials are in tune as well as the fundamental. Randy once told me that he thought that any Selmer Mark VI could be made to play in tune if it is just set up properly. Sometimes in order to fix intonation problems extreme measures, like building up the insides of tone-holes, need to be used .
The techs that I know on the west coast who a good at setting up a horn are Lee Kramka (Sax Worx) in San Francisco, Eric Drake (Saxology) in Berkley, and Sarge (World Wide Sax) in Everette, Washington. In Colorado there is Tim Glesmann (Sax Alley) and of course in Boston there is Emilio Lyons. I'm sure there are more but these are the guys I know who are really good.
Both of my horns need some help with key height regulation right now. I may drive the three and a half hours north to Everette to see what Sarge of World Wide Sax can do with them. Sarge can bring trashed horns back from the dead to look like new. My Mark VI tenor is wildly flat on the high F#, sharp on the palm keys, and the overtones aren't even close to lining up and my altissimo G barely even comes out. I do like the horn's sound, so I'm going to give Sarge a chance before I trade it in for a different horn. On my alto my low C is really sharp, as well as my palm keys.
My point here is that not all intonation problems are caused by the player. If your horn is not set up right it can be nearly impossible to play in tune. You may want to consider getting an expert repairman to check your key regulation out, even if all your pads are sealing.
It never seems to end.........