I got pretty sick not long after I started flying. I discovered that I got a bug from a layover in an 'exotic' destination. It took months to completely shake off and quite awhile to work out what was wrong with me.
It's quite normal to be sick in your first year of flying or for your first time doing shiftwork. My advice to anyone is just go and see your doctor and no matter what do not operate when you are sick. A friend who had more experience in flying gave me this advice and I wish to hell that I had taken that advice earlier!