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I too am taking progesterone and it hadn't affected my cycle until this month - I was around 3-4 days late and had awful cramps and starting with very light brown spotting, I too had thought I was pregnant but all tests I took were negative - I just think changes can occur in your cycle due to stuff out of your control and it is VERY frustrating but hang in there!
Hopefully, it' good news for you, though :)