I recently had to take my scanner bed apart to remove some water that had gotten under the glass. When I put everything back together, the scanner doesnt seen to be able to find its home position. Does the light unit need to be placed on the belt at a certain position? Does the timing wheel on the end of the motor that drives the belt have anything to do with it. I dont think there was any damage from the water, it just acts like it lost its timing.
Unfortunately in a situation such as this, if the hardware does not fit together as it sould I would refer you to a service technician as these damages are not covered under the manufacturer's warranty.
I would suggest removing the scanner glass again and then cleaning the white strip on the underside of it (this should be what the scanner checks against to find its homeposition). Also (gently) clean the scanner lamp and mirrors as they might be dirty or have condensation on them.
If it still won't work after you re-assemble it, then it might be a more serious issue and like AlwaysNeon suggested, taking it to a service technician would be the way to go.
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