In the winter, your heating system and the outside air has a lot less water in it than in the summer. Your wood absorbs the humidity in the summer and expands. Some of it has no place to expand because of the filler so it permanently shrinks the wood by crushing the cells in the wood. Then you have another winter with it's dryness and the wood shrinks. Since some of the wood cells are totally gone, cracks appear. If you fill these, the cycle starts over. You will never be able to totally stop this unless you maintain contstant temperature and humidity.
Hot wax poured all over both sides of your wood would eliminate the problem since that's about the best there is at stopping water vapor exchange. The problem is that this would not be a very attractive or practical solution. Polyurethane is about 35% less capable of stopping the moisture exchange and offers an attractive and easy to apply solution. Personally, I much prefer oil based poly's but they do take a long time to dry and more time for dust to collect, which it does. At the same time, I think that the oil based offers more cabability to withstand kids, dog's, cats and the like.