In the flash shoe on the top of the camera, there is a metal spring plate. Under the plate you will find a white cylandars that goes through the hot shoe (about as thick as a paper clip). When an external flash is pushed onto the shoe, this pin is pushed down and tells the camera there is an external flash in the flash shoe. This disconnects the internal flash. Spillage can cause this pin to stick down. Remove the battery, and then put a little Windex on a clean toothbrush and clean the pinhole. Blow lightly to evaporate. The pin should pop up, but it might take a couple of cleaning attempts. Another cause could be that sticky liquid spillage has gotten on the pivots for the flash. Once again, cleaned with small amount of Windex on a q-tip may free the pivot. One of the pivots is a screw. Sometimes it is rusted, and needs to have the rust scraped off and then a light coating of grease applied.

This can also be caused by shorting out the circuit with flashes. If the flash has power on when put on or taken off, and the central sync contact on the flash touches either of the two dedicated pins in the back, it will damage the circuit. In most cheap flashes (and almost all old ones) the full voltage of the flash (over 300 volts) is on the sync contact in the center, and there is a switch in the shutter that causes the circuit to complete. Later flashes used a 3 volt sub circuit to complete the circuit, isolating the camera from the full 300 volts. If the flash sync contact that has 300 volts touches either of the dedicated pins, then you have 300 volts going into a 6 volt circuit. This usually damages either IC3 (PX3) or both IC3 and IC2 (PX-3 and PX-2). These parts haven't been available for nearly 15 years. Damage to these pins can cause problems like the aperture opening all the way or closing down all the way every shot, or the curtains traveling together every shot (blank shots).

The sensor for the flash is actually the clear frame around the flash tube. There is a black 'wire' attached to it (actually a light pipe) that attaches to the frame and then goes back to the 'sensor' at the rear of the flash base (the part that flips up). Pop up the flash and remove the screws underneath to remove the top cover of the flash and make sure the 'wire' is in place. Caution: if the flash is on or has been used before there is over 300 volts across the flash tube. Do not touch either end of the flash tube or you will get a nasty shock.

You do not mention what lens you are using, but the most common lens you see with D90s is the 18-135, and on that lens focusing in and out can be caused by a failure of the magnetic sensor on the side of the lens, or a failure of the lens circuit board. As Nikon has stopped selling parts, your best bet is to first check the camera with another lens. If it works OK with another lens, then send in the bad one to Nikon.

Nikon stopped selling parts in June 2013