The flush from niacin is caused by vasodilation and a histamine dump. When trying to use high dose niacin you need to very slowly work up your dose over weeks. What happens is that it eventually depletes you body of histamine and the flush is greatly reduced. I hardly get a flush at all with 1000mg.
Important note however, if you miss a dose your body has time to replenish histamine so you need to cut back and work up again. The more doses you miss the more you have to cut back and work up.