The first one is the January 17th 1996 workprint, the second is the Digital Domain workprint which has the special effects cleaned up.
Notice that the Mini-Hunter is different:
A large difference. When Arnie approaches the wall in the January 17th workprint, an Aerial Hunter-Killer flies from the left to the right, and whlie the camera zooms in, another Aerial Hunter-Killer leaves the SKYNET complex, but very late (in the pics it's just a dot but it quickly flies towards us).
In the Digital Domain workprint, the first Aerial Hunter-Killer (from left to right) is gone and we immediately see the "other" Aerial Hunter-Killer appearing from the SKYNET complex.
