Are you 100% sure you are not pregnant? If there is a possibility no matter how small you may want to do a test just to clear that up.
I don't know whether LT could mess up your menstral cycle, I have had no change in mine. I think you should have a word either with LT directly on 0800 413735 or speak to your pharmacist or GP. You should check it out just to be on the safe side.