Let’s start with a crack in the top the first winter that it is put into use. This crack developed because the air was drier than the wood, so moisture left the wood and the wood shrank, or tried to shrink. As shrinkage increased or attempted shrinkage increased, eventually, the stress became so high that the wood broke. (A glue joint is 1-1/2 times stronger than wood, so the glue joint should never crack unless it is inferior—poorly made.)
In the summer with the more humid conditions, the top wants to swell and so will close the crack back up. In your case, however, the epoxy repair makes it impossible for the wood to close the crack the first summer after the repair. So the wood tried to swell and being unable, it created pressure. This pressure caused the wood cells (hollow tubes is what the cells look like) to be compressed. So, in the late summer, the wood fit around the repaired crack tightly and looked good. The compressed cells are essentially compressed for life (unless subjected to wetting with liquid water).
Now, when the drier wintertime came again, the wood wanted to shrink a bit as it dried, and with the compressed cells, any shrinking resulted in an increase in the size of the repaired crack beyond the size of the crack the previous year. We could say that the crack “grew” larger because of the repair. Without the repair, the summer swelling would have closed the crack and then winter shrinking would have reopened it back to its "normal" winter size.


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So, what you need for a repair is something that will give and take easily as the wood naturally moves from summer to winter to summer to winter (humid to dry to humid to dry) annually. Another piece of wood glued into the crack is a good idea if it can be glued in and if it is not installed in the middle of winter when the wood is the driest. A second option: Putty will work, except that it must be flexible, which means in the summertime it will be squeezed out as the crack closes forming a ridge (objectionable?) and then go back flat in the wintertime as the crack tries to open. Neither option seems too good.
A third option is to initially let the entire panel move without restraint. That is, the best option is to design the fastening system to allow the entire panel to move seasonally rather than trying to hold it and prevent movement. This floating, along with a good finish, top and bottom, that will retard or buffer moisture changes (there are no perfect sealers for wood) is the best we can do. A simple system uses screw holes that are slotted and screws that are not too tight so the screws will move within the slot as needed. Of course, there may be a crack between panels or at the wall, so molding is also a good idea.
Note 1: Wood is wood and we cannot stop wood from moving unless we have a constant humidity year round. The maximum movement is when we use the end grain design you have, as each piece is moving in both directions. With long, edge-glued strips, there is no (or rarely very slight) movement in the lengthwise direction, just across the grain.
Note 2: Epoxy must be a thick joint to develop strength. If it is too thin, there will not be enough heat generated to thoroughly cure the epoxy. Oftentimes, a repair uses too much pressure giving a weak joint.
Note 3: Remember that wood does not shrink unless its moisture changes. The development of a crack is evidence of shrinkage and so we know that the moisture was higher, prior to the development of the crack, than it is now. You can measure the MC now, but that does not tell you what the MC was. For that reason, it is critical to take MC readings prior to shipment. Do not assume that the wood is 6.0 percent to 8.0 percent MC or that the wettest piece is no wetter than 7.5 percent MC. Measure the MC yourself and record the values- -measure the incoming lumber’s MC and the final product’s MC, and even measure MC during the manufacturing process. Also, measure the plant humidity and make sure it is no more humid than your customer's home or office (oftentimes 30 percent RH or even lower in the wintertime). Humidifying a shop in the winter can reduce problems in manufacturing, but actually, it often just pushes the problem to the customer, and then it is really expensive to fix compared to catching the problem before shipping or getting lumber at the right MC right away.


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