You know those bars that appear in some games? The ones with an arrow moving back and forth along the bar and you have to click at the right time to make the arrow stop in the green section of the bar but not the red section. I think the Shuffle catch rates work like that. Imagine that there is an invisible arrow moving across the catch rate bar and lets say you have a 25% catch rate, that is the green section, and 75% of the bar is the red section. When you tap the Pokeball you stop the invisible arrow on the somewhere on the bar. That's why you can fail with 90% because the arrow lands on the 10% you don't have, and that's why you can catch with 5% because the arrow lands on the 5% you do have. It all comes down to luck, that's what I think anyway.