Hookay, I’ll see what I can fit in here before my computer time (at the library) is up:
Back to swelling boxwood tenons to start (will address the “wax on the cork build-up issue” as time allows):
Clark,
As I mentioned, the problem you’re having is that the tenon is absorbing moisture as you play. The spit… er, “water vapor” 
and water, enter through the end grain on the edge of the tenon joint, as well as through the bore inside the tenon. In the short term a (boxwood) instrument with an unsealed bore and end grain will swell quite rapidly, and then shrink back to the normal size somewhat less rapidly. In the long term you can suffer permanently out of round tenons (very bad because they can become so out of round you won’t be able to put the flute together) and or cracks (actually, somewhat less bad in many cases.)
Many makers who use Boxwood on a consistent basis seal the bores of their instruments as part of the standard process, others seal both the bore and exterior, which is what we typically do at vH. For some reason I was thinking that I had heard Peter Noy did seal his Boxwood instruments, but perhaps not, you should contact him to find out. Unfortunately, some makers of “Irish” style flutes don’t do any sealing. I think this is simply because they don’t get much call for Boxwood flutes, and so don’t have a lot of experience with the wood, which is understandable.
You can sand some cork off the tenons, which will, for now, improve the socket/tenon fit, and reduce the chance of cracking a socket or tenon, but of course this just treats the symptom, rather than the disease.
Okay, then how do we treat the problem? Well, as things tend to go in circles a bit, this takes us back to oiling, among other things, and although I normally recommend against it, you could oil your flute daily, which aside from being messy, is a pain. Frequent oiling will slow the rate at which water gets into your flute, not so much because it’s a barrier (studies show most oils are virtually transparent to water vapor), but rather because the water must displace the oil, before being absorbed.
So, I’m contradicting myself, right? I mean I did tell you not to oil boxwood like crazy, didn’t I? Yes, I did say that, and I stand by it, as long as you aren’t having radical swelling problems. However if your instrument wasn’t sealed, and the wood is going radically swelling when you play, then one valid option is oiling constantly, but it’s a short term solution, and no guarantee, so proceed with the oil bathing at your own risk. This will, over time, change the color of your instrument pretty radically, btw.
Another safe trick you can try is to buy some extra thin superglue and apply over the end grain of the tenon, just on the very edge. Apply one coat, let dry, and then repeat. This should help some, won’t hurt the flute, and is reversible, however I’ve had mixed results, with this approach, and I’ve rarely found it a complete solution.
The best long term solution, in my experience, is to completely seal at least the bore. As I’ve said, we’ve learned over the years that this is a must on all boxwood instruments, because the wood is naturally just too reactive to changes in humidity, even when the wood has seasoned for over 20 years. I can tell you that proper sealing positively works the vast majority of the time, because I consistently see instruments (ours and other makers) that were made, 15, 20, and 30 years ago, and typically the ones that have been sealed are in excellent condition, very little warp age or cracking, while the unsealed boxwood instruments virtually always have significant issues.
Clark, at this point my advice would be to contact Noy and see if he would be willing to seal the bore of your instrument. I know it won’t be much fun to ship it off for a while, but in the long run, that’s the best “permanent” fix, IMO. It may be tempting (for some folks) to try bore sealing at home, but I’d really recommend against it, particularly on keyed flutes, it does take a bit of experience to get right, and some sealers are permanent, so if you do a poor job, you’re stuck with the results.
Good luck Clark, and let us know how it turns out.
Loren
P.S. Sealing a flute’s bore typically will change the tone a bit (for those who are sensitive to such things Typically, with boxwood, the tone becomes somewhat harder and more focused, just how much depends on the sealer and the coating thickness.
P.P.S. Wax and cork grease can build up on corks causing a tight fit. It’s usually a good idea to clean your corks thoughroughly before sanding - often instruments come across my desk with complaints from the owner that the socket/tenon fit is too tight, and it is, however once I clean both the socket and tenon and cork, the fit is usually just right, or even a bit loose! 
So I’d suggest folks don’t start sanding their corks until they are certain the tight fit isn’t due to build-up o
].
