It throws mine off too. I've noticed when I don't masturbate my period comes on time, like clockwork. I abstained from masturbating for a while to test this. I then realized that if I masturbated during my period or within 5 days after my period my next cycle would not be thrown off. I have no idea why it effects my cycle and ovulation for me. My period is usually thrown off 5 days after my last cycle ended (ex: start the 12th end the 16th, masturbating: start the 21st) if I masturbate anytime. Weird, but a pattern I noticed.

No, it shouldn't. I've been doing it for many years and my period is quite regular. You might want to go see a doctor and make sure everything is alright. I have heard that masturbating during your menstrual cycle will help calm the cramps, though. Never tried it, probably just a myth, but that's the only thing I can think that may relate. Other than that I don't think there is any correlation.