Miles are usually credited when the flight coupons are lifted. With paper tickets, I am guessing they lifted your flight coupons at check-in, so when tabulated all the flight coupons after the flight pushed back, your coupon was there, so you got the miles.
With e-tickets, "flight coupons" are lifted/processed after pushback by the computer.
Even with paper tickets, you would only have the flight coupon of your first segment lifted - so you'd only get miles for your first segment.