From the OP:
Question: Help! Why don't my animations line up?
A) If you are on uneven ground, too close to another object (walls, stairs, chair and so on) it can screw up the alignment. If none of those are the issue then just hit the 1-4 or 9, 0 keys at the top of your keyboard to adjust the alignment while your PC is having sex. Any changes you make will be saved in your saved game. If you start a new game however, those changes are lost and you will have to adjust them again.
As pointed out above, all animations are based on imperial height, so if you or your partner are not imperials, then some adjustments may be needed.