When the Tardis materialised on the Earth all those years ago, the chameleon circuit fused, locking the Tardis into the shape of a Police Box. In order for the chameleon circuit to work it has to know where the Tardis is going to land, so the navigation system has to run through it along with temporal sensors so that it can identify where its going and its surroundings.
Now the circuit fused, but its still working. Otherwise the Tardis would just look like a big grey box. So that means its locked into the image of something from the Earth. This must be causing feedback into the navigation circuit. Thus the Tardis has a predilection for landing on the Earth, even when the coordinates are completely random, because that's where the circuit feels it blends in properly. Even when not on Earth this would cause the Tardis to pull to places it feels more comfortable. So, landing on Earth like planets and when heading for a completely different planet, this pull from the circuit should be enough to send her way off course.
So, the navigation system is probably fine. Its just that the chameleon circuit is telling it where to go rather than the navigations system telling it how to look. The Doctor just needs to route the navigation circuits around the chameleon circuit and he should be fine!