I'm fairly well read on the subject of the human sleep cycle and all related matters.
I also have a good deal of experience with hypnagogic/hypnopompic jerks, paralysis, hallucinations, and other artifacts.
It's never really bothered me, though this is probably largely in part to me knowing exactly what they were before I even experienced them the first time.
In my experience, hypnic jerks are caused by one of two things.
1: The process of falling asleep.
2: An event in a dream that triggers a reflex. (falling down, getting hurt, etc...)
When falling asleep, your muscles begin to relax. This relaxation can sometimes be interpreted identically to a loss of balance by your nervous system, so a reflex is activated which makes your muscles jerk and go rigid (like when you normally lose your balance). This awakens you, and makes you feel as though you just "fell into bed". (I used to have a source for this, but I can't be arsed to find it, ATM.)
In-dream events that would normally trigger reflexes in real life are able bypass sleep paralysis because they work on a different muscle freqency.
This explains dreams where you trip/fall/get hurt, and then suddenly awake and have the same feeling of having fallen into bed.
