Generally ...
Niacin comes from in several forms: (1) “true niacin”/nicotinic acid, (2) nicotinamide (also known as Niacinamide), a nicotinic acid amide, and (3) other derivatives (such as inositol hexanicotinate).
Niacin in the form of nicotinic acid can lower triglycerides and increase high-density lipoprotein. HDL helps remove low-density lipoprotein (LDL) cholesterol. Niacin/nicotinic acid is a B vitamin that's used by the body to turn food into energy. It also helps maintain nervous system, digestive system, and skin health.
As to its cholesterol benefits, Niacin/nicotinic acid can allegedly lower triglycerides by 25% and raise HDL cholesterol by more than 30%. The skin flush that may result from Niacin/nicotinic acid is the result of vasodilation.
Although it is similar in structure to Niacin/nicotinic acid, Nicotinamide contains an amide group absent in nicotinic acid -- the addition of that amide group alters the therapeutic effects. Niacinamide, does not have the same vasodilating effect that Niacin/nicotinic acid has, thus it does not have the same skin flush as Niacin/nicotinic acid.
So, that amide group addition in Niacinamide is the reason that Niacinamide does not impact cholesterol in the same way as Niacin/nicotinic acid.
As to the specific reasons this is the case – well that is way beyond my (novice) level of understanding.