i did wonder if that was the case but do you use the same filler over the skirting or very carefully use wall/wood filler?
(sorry for all the questions, just interested)
On the wood work i might use a tiny bit of wood filler to feather it in at the edges, on the walls, wall filler to feather. I try to not put a hard filler over the flexible one where you would expect movement.
I think I got better at it, elsewhere in the house it didn't seem to take as long and it still hasn't cracked.