Yeah, that Uncollected checkbox can really trip you up. We need a better solution for saving whether a user wants it on or off by default. There are actually 3 user stories with competing needs:
New User: Wants Uncollected off because they don't own very many cards and they want to make a deck with the cards they have.
Advanced User: Wants Uncollected on because they have a large collection and will craft what they are missing.
Uber Power User: Has all of the cards and wants Uncollected off to hide Planeswalker deck cards.
Thanks for posting your experience, it's something we are working on!