I would recommend an STI check.
A friend of mine had recently started a new contraceptive pill, following a break from hormonal contraception. She used to take this same pill (but different brand) for years, then tried a mini-pill, then had a few months out. Started it on day 1 of her cycle, and first month no problems. She then experienced really erratic bleeding and really bad period pains to the point where she was physically sick, having never really suffered with pains before.
It turned out her new partner had given her chlamydia and she'd got pelvic inflammatory disease - which can cause fertility problems if left untreated. Luckily she caught it quick and is fine, but chances are with your body if something doesn't feel right it isn't. It's always worth getting stuff like this checked out! I know I would now after what she went through!