Red-eye is caused by the light from the flash reflecting from the back of the eye. There are several ways to eliminate or at least reduce the effect. One, as you've done, is to edit the photo after it's been taken. The red-eye reduction feature of the camera shines a light at the subject, causing the pupils to contract and thus reduce the reflection from the eyes.
A good way is to move the flash away from the camera. This causes the red reflection to go toward the flash, not the camera. Unfortunately, the D40x lacks the Commander mode to control remote flashes. Instead, you can use something like the SC-29 cord to move the flash away from the camera.
Another possibility to consider is to not use the flash at all. Bump up the ISO and see whether there's enough light for existing-light photography.
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