This is just a guess and not specific to your bike. I'm also not sure if the effect is large enough to be noticeable. So, just my theory:
In the bowl of a carburetor, there is a float, pushing a valve up against the fuel inlet pipe. So it closes when fuel is at a certain level in the bowl.
Now, fuel finds its way into the carburetor by gravity only. And if the tank is full, there is more pressure at the fuel inlet, and it needs more force from the float to close the valve. This means, the fuel level in the bowl is a little higher when the tank is full, and a little lower, when the tank is almost empty. And as consequence, the mixture is leaner when the tank is empty.
And a lean mixture could cause the effects you observe, though it's hard to believe that the effect is so strong.