When routing, pins and vias are selected and snap to connect point is enabled. The problem is not the initial routing. The problem is that traces that were initially successfully routed (meaning the ratsnest goes away, the trace is on the same net as pins, and the trace stretches and moves with a symbol it is connected to) become unrouted sometime later. The trace does not go away, it is just no longer connected to the pads (meaning that there is now a ratsnest again and the trace does not move with a symbol). The trace does still have the correct net and appears to be over the pin, however. This is happening to hundreds of connections over and over again.
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