When something just isn't clicking in my brain I move on from it! Then some time later (not a fixed time) I happen across it and read through it again with a fresh mind.
This has happened too many times for it to be a coincidence, that the 2nd attempt ALWAYS makes things click very naturally. It has happened with probability concepts such as Bayesian networks or HMMs, optimization algorithms like EM, Monte Carlo sampling, bootstrap, functional programming concepts like monads, C++ move semantics; the list goes on.
Whenever you're stuck, just take a break! And not a 30 minute coffee break but still at the back of your mind kind of break - completely forget about it and come back in a few days, a few weeks or even a month or 2 later