it sounds like you are not gettng an uninterrupted flow of clean fuel to the carburator.
Check the gastank cap for a clear vent hole. If it gets clogged the tank develops a vacuum. Also remove the petcock and check the filter and/or screens for crud. Check any other fuel filters and the fuel lines.
Another thing could be contaminated fuel. Water in the fuel, or sometimes even 2-stroke oil (is that bike a 2-stroke?) can cause problems.
One time i had a similar problem. For some reason, the 2-stroke oil was seperating from the gasoline and i found small globs of oil in my float bowl. When a glob of pure oil was sucked into the engine there was a hesitation.
The float level might be low or the float needle could be sticking.. If the carb was replaced with an identical unit i would not suspect that the float needle orifice is too small for that engine...
Of course make sure you have enough fuel in the tank. When the tank is near empty, you can get air bubbles in the lines.
Theres a million reasons .. these are some of the easiest ones to check.