I've had that happen a few times on my orange one too. I think the reason may be not enough water when the stem is first forming. I always keep my plants very dry from Oct - Feb. That's supposed to be their rest period. If I don't start increasing the water when I first notice the flower stem, the stem always remains short and the flowers open amongst the foliage - very icky.
I've never confirmed this theory with anyone else or any clivia research, but that's been my experience.