Hey, just joined the community!
Anyways, for anyone who's had this problem before--> Your model (like a monster_scientist) which u gave a sitting animation "snaps" or "skips" after having completed that animation to the point where his model is placed in Hammer.
Here's the solution that made it work for me, after experiencing that problem: use the monster_sitting_scientist, instead of the other model, because the monster_scientist starting position is a standing pose, and thats why you might see him shortly in the air, before the game drops him down again.