Cracks in wooden flutes can occur for two reasons. Firstly they can develop in the seasoning process of the timber. This is one of the reasons that timber suppliers wax the ends of the billets, because moisture leaves the wood much more easily via the end grain, and if this happens too rapidly it can lead to cracks.
If these are big enough, then the piece will be rejected in the manufacturing process, but what can happen is that a very fine crack will go undetected until the flute is finished and begins to be played. Then the stress caused by the timber absorbing water and drying out again, as happens in the normal process of playing, can cause this minor cracking to quickly become bigger. If this is the reason for a flute joint cracking, then it generally appears very soon after the flute arrives from the maker and begins to be played. It's also one of the reasons why it pays to play a flute in gradually.
Cracks which develop later on are generally due to water stress, typically caused by a combination of not playing on a regular basis, playing for long periods of time with out swabbing out the moisture, and storing the flute in conditions which are too dry. Essentially it's moving the timber from very wet to very dry conditions too quickly. Physical stress may also result from this as when a swollen tenon can crack the socket.
The metal lined parts of the flute, the head and barrel, tend to suffer more from this, as wood trying to shrink over a metal tube has "nowhere to go".
Fixing cracks is one of the commonest repairs that the flute restorer has to face, and unfortunately is also one of the most misunderstood. The two commonest methods used, filling the crack, and glueing the crack are unfortunately also the two most unsuccessful.
Putting material into a crack can on a short term basis solve the problem...particularly if air is leaking from the crack, but although a soft material such as beeswax will not cause this problem ( it causes others) a harder material, such as the commonly used epoxy, essentially only serves to push the two sides of the crack further apart. It may take some time for this to happen, but if you look carefully you will eventually see very fine cracks developing, one on either side of the filling material.
So in attempts to avoid this the idea of gluing the crack closed arises, and in fact some fillers are glues in their own right, such as the epoxy mentioned above. The problem here is that the types of timber that flutes tend to be made of do not glue at all well, and given the fact that by the time the repair is attempted the internal surfaces of the crack are usually covered in oil or grease, the chances of any sort of permanent adhesion are extremely low. It must be remembered that the forces that cause the crack in the first place are extremely strong, and even if there was good adhesion it might not be sufficient to overcome them.
Again, if an old flute is repaired by this method, it may hold for a while, especially if it's not played much, but eventually cracks will appear again between the glue and the timber.
The technique that I use involves threading, but this time of the sewing variety. A bunch of threads, the number depends on the size of the drill used and the thread thickness, is pulled into the hole until about 20mm still protrudes. A drop of superglue is applied to the thread, and this is then rapidly pulled into the hole. The result is that the pressure causes the glue to set almost instantly, resulting in a hard pin which is glued into the hole. The ends are cut off, and the process repeated.
The reason that this is such a successful method of crack repair is that the pins act directly against the pressure caused by the crack wanting to widen, and the area of glued surface which resists this is vastly bigger than just putting glue on the sides of the crack, which of course also happens in this case.