The problem is that food thieves are very entitled people. Signs, attempts to shame them into good behavior, appeals to their better nature - none of these work because they just don't care. If the person you suspect is the thief, he may even feel that he's earned the right to scavenge food - after all, he's there working late on Super Big Project. Look how hard he works, the sacrifices he makes! What slackers everyone else are, going home at 5! He needs to eat when he's working so hard, and he just can't spare the time to go out and get something, or bring enough food from home.
I would be very surprised to see a company fire a manager for taking food. That might be the final straw in a long list of other issues, but I can't imagine that would be the only reason. As he's above you in the food chain, accusing him directly wouldn't be too productive and could hurt your career at that company. You can't *make* him stop stealing your food. It stinks, but there it is. The only solution I see, as others have suggested, is to keep your food at your desk during the day, and lock your desk at night. If your desk doesn't lock, take your food home with you every night. It stinks, it's unfair, the guy is a total jerk and it would definitely affect the way I felt about him at work (no special favors or rush jobs for you, buddy), but I don't know that you have other alternatives.