I've a simliar problem. Two thoughts: A), let the wood re-absorb moisture and swell again, then paint or varnish, or B), fill with a flexible filler or Epoxy, and varnish. I've just epoxied a big crack, (and then read how to do it in PBO... ) I think, by the fact that the wood is unpainted, it'll dry out far more than if it had a coat of paint or varnish. Not seeing the situation up close, I'd epoxy it and then varnish. I know you've done that already, so you have to stabilise the shrinkage. Either the wood was too damp for the epoxy to bite well on the wood, or there just wasn't enough in the splits. You could cheat by filling the gaps with brown Sikaflex or similar. This would keep the water out whilst you let the wood get damp enough and swelled again.
-------------------- "Let Joy be unconfined!"
I'll get her chastity belt keys, then..