Whenever I get a weird feeling about someone or something, there usually is a reason for it. I attribute it to having been around a lot of dodgy people and dicey situations, and that certain conditions will trigger a sense of something not being right.
For example, a former co-worker set off this feeling on the first day I met him, and I told the boss about my "funny feeling" about the new hire. About three months later, we caught him snoozing in his car, reeking of alcohol. Then we spotted some office equipment in the back seat. He had stolen it from the stock room and passed out before he could even start the car.