Sleep apnea is an interruption of/in breathing during sleep. There are three forms of sleep apnea: Central (having to do with the brain's signal to breathe) Obstructive (having to do with physical obstructions to breathing e.g. snoring) and Complex/Mixed (a combination of the two)

I don't find amnesia mentioned anyplace as a symptom of apnea.

People with apnea often snore and/or awake in a start; is that happening?

Have you checked any medications you may be taking for side effects involving memory?

These times that you awoke and lay in bed for several minutes - were you able to move or did it seem like you were paralyzed?

How long has it been between your injury and these episodes manifesting?

I just found this; does it sound similar to what you're experiencing?
http://en.allexperts.com/q/Sleep-Dis...a-Awakened.htm

See also:
http://en.wikipedia.org/wiki/Transie...leptic_amnesia

(just a couple of wild guesses)

Doc