This answer matches my experiences very closely. When you feel you brain begging you to gloss over the equation and move on - that's a red flag that you need to slow down, exercise discipline over your concentration, and figure out what's going on. It might take a few days for the intuition to settle. Personally I've known it to take a couple of years.
edit: patience, self-forgiveness, and a willingness to accept frustration are important traits. You might spend a whole week banging your head against the wall, feeling like you're making no progress, and then one day everything falls beautifully into place. That doesn't mean you did something correctly on the final day - it means you did everything correctly for the whole week before. Don't view a difficult and unrewarding day as wasted time. You're building something very difficult and that takes a bewildering amount of time.
edit: patience, self-forgiveness, and a willingness to accept frustration are important traits. You might spend a whole week banging your head against the wall, feeling like you're making no progress, and then one day everything falls beautifully into place. That doesn't mean you did something correctly on the final day - it means you did everything correctly for the whole week before. Don't view a difficult and unrewarding day as wasted time. You're building something very difficult and that takes a bewildering amount of time.