Go to the Scene where Neo and Trinity go into the compound and they go through the metal detector. When Neo shoots the guard, the gun is black, but two seconds later when he drops it on the ground it's silver.
P.S. I'm not sure, but it might be vice versa (guns first silver then black.)
I have just watched the movie and the gun is indeed black when he shoots the guards, but it is also black when Neo throws it to the floor. It just picks up reflections from the lights on the ceiling. the same effect can be seen in the Matrix Construct(the scene where Neo finds out what the matrix really is) in Morphius' sunglasses, or on a piece of black plastic reflecting light.
Nope. The guns are black the whole time. What you're seeing is light reflecting off the polished black of the gun. Trinity's black leather also reflects light in a similar way.