My experience of The Spellcoats was pretty much exactly the same as yours - I always used to feel very stupid that I didn't get some of DWJ's endings, and it wasn't until I was an adult discussing them with other fans I realised it wasn't just me.

When the Crown of Dalemark was published, they re-released the other three as well, and I found them when I was supposed to be in the middle of studying for college exams... I'm sure it didn't do my results any good, but I still have the books.