I originally posted this as a question, but I deleted that thread because I figured it out myself. Nobody had seen it and replied to it yet anyway. But I figured I'd post this just in case someone else is confused about the same thing as I was.

I originally did a complete playthrough of all four episodes, including the wormhole level, and had gotten all the other achievements, but the Crystal King achievement wouldn't pop up to grant me the 100% completion. The crystal counter stopped at 4,989 crystals out of 5,000. So I originally posted a question here, asking what I was missing.

But I went back and tried something. I started a new game (on the fourth episode, but it might work regardless of which episode you choose), and selected Hard Mode (that might also be coincidental, and you might only need to start a new game in general). I went into one of the levels, and as soon as I had picked up 11 more crystals, the achievement popped up.

So in short, if you playthrough it all, but haven't gotten this achievement, start a new game, and you'll get it eventually.