I've had this annoying problem for a long time, and then accidentally found the solution, so thought I'd share it here in case anyone else has the same problem.
Problem: When I create a custom workspace with palettes where I want them, sometimes on launching apps (illustrator and indesign) the palettes would be missing or the collapsed palette button will not respond to any clicks. Often have to restart the app several times.
Solution: Not sure if this is a bug, but it's the "application frame" that's the culprit. I always had the Application Frame off. But when I turn it back on, all palettes now appear and function normally.