I think logic dictates the blood came from the numerous lacerations (see the excerpt I posted at #75) she suffered. There was no testimony that she was having her period, and she did get examined, so I would think that possibility must be discarded (plus it would be unlikely she would consent to intercourse if she was). In fact, Mackey would have used that if there was any evidence indicating it was menstrual blood.
I bet there's a way to tell if blood was from the cycle or from an injury. It's not just blood in a cycle, there's a sloughing off of tissue, too. And don't forget the vaginal tearing involved. Finally, if there was an issue of the victim's cycle being involved in the bloodstains I'm sure Kobe's lawyer would have brought it up. Since she didn't, I'd assume the defense isn't disputing that the blood came from sexual activity.