It shouldn't. I've never heard of this happening.
If you read the STD facts about chlamydia, sometimes it'll cause bleeding between periods, or it'll mess up your cycle a bit. I had it from my ex, didn't know about it for a year..(as he thought it was MORE important for him to be treated than for him to let me get treated also..), and I ended up skipping a period. I thought I was pregnant, that's why i got tested. I had chlamydia. It sucked.
From my personal experience, I would take a pregnancy test first, THEN and ALSO get tested for STD's. It's always good anyways to be tested every so often.