Falling damage seems to have become much more strict since at least 1.3.2. The patch notes don't seem to indicate any increased penalty for fall damage or the heights that should be causing it.
Comparisons for 1.2.5, 1.3.2, 1.4.2:
1.2.5: Seemingly normal fall damage behavior
1.3.2: More random fall damage, specifically with 3 block falls which aren't supposed to deal fall damage. Damage seems to occur from the fall about as often as it doesn't.
1.4.2: Consistant damage from 3 block falls.