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Missed period for two months after protected sex

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My boyfriend and I are long distance at the moment and we only see each other like every two to three months for about a week. We obviously have sex during the week we are together. However after this, I miss my next two periods, but after a week when I should of started, it comes back. (Sometimes there is extremely light spotting, but it will last like a day) I am on birth control pills and we always use protection. After I miss my first period I will take a least two pregnancy tests and they always come out not pregnant. I'm not sure if I should be concerned and see a doctor. Do you know whats happening? When we were together consecutively, before I changed colleges, the sex never messed with my menstrual cycle.
Thanks!
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