If you are on birth control, I would think it is unlikely that you are pregnant, (because most methods are very reliable being up in the high 90%'s for reliability) especially as you are saying that all your tests came back negative. Although it does happen from time to time.
Being ill could be a side effect of the pills, or like you say it could be a stomach bug, or maybe just an upset, but if you are being sick this could reduce the reliability as you might not be getting the whole dose into your system.
If you were having sex during illness did you use a condom as back-up?
Being ill can apparently mess up your periods, I suppose periods can sometimes jump randomly too (I've known mine come over a week late on a couple of occasions, mine are quite often early or late, rarely follow an exact pattern), so it could just be a "blip".
I don't reckon you need to worry too much, but then that just my personal opinion.
Go with your instincts, if you are really worried then go and see your doctor to put your mind at rest.
Good luck!