I believe it is just fatigue of the muscles being dormant. Your body goes trough a cycle where it adjusts it self over time until it finally wears down creating charlie horse. Similary to earthquake fault lines building pressure then releasing with a quake.

I think Frankie is on the right track. I think they are usually caused by muscle spasms and usually because you have not stretched properly before AND after exercising. The best way to prevent them, of course, is to do the proper stretching exercises.
Also Frankie mentioned a mineral deficiency. The best way to handle that is to take, for example, a TUMS or a mineral-enriched vitamin before you go to bed.