Gaining weight

I have been using a compounding pharmacy bio identical progesterone cream for over a year without issues with my weight until 2 months ago. I was using it twice a day and once a day during my period. Recently I stopped using it during my period because I was getting stomach aches from the up and down levels of progesterone from only using it once a day, and immediately I gained 3-5lbs. within a week. I run 5-6 miles a day and eat a healthy 1200 calorie diet. Did this happen from the change in my usage, or from missing the progesterone during my period?
Thank you for your time :)

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