Of the two, the radar is the most accurate. AIS isn't broadcasting every second and transmissions rate can change as it has to wait for other AIS traffic taking it's turn. A boat can move some pretty good distances between transmissions. The AIS location is also entirely out of your control. That location is what the other ship is transmitting. Some very large tankers might have that GPS at the front or the back of the boat. When they are 600ft long vessel that is some additional distance right there on top of the other factors. Radar as long as you have it properly aligned to the bow of the boat and the heading you are using is good, it the best source of the other boat's current location. If your heading data that is being used is off somewhat because a flux gate is being pulled it is just one more thing that leads to them not aligning perfectly. Sat compasses give the best option for your heading information as they are not dependant on magnetic north. There is a lot of variables to consider but it isn't abnormal to have several targets (AIS and ARPA) not be directly showing on top of each other. One must just ensure that everything is correct as possible and understand that the radar is more Realtime data.