The negative probably needs to be back lit instead of front lit in order to scan right. You could take apart an old scanner... cover up the light bulb with something to prevent it from lighting up x-ray. You could try taking out the light bulb and hope the scanner doesn't complain. Then you would need to figure out a way to light up the x-ray from behind. You might be able to get it to look good with both front and back lighting... so the scanner mod might not be necessary.
Laptops and LCD displays tend to have a plastic light diffuser that spreads the light out evenly across the entire surface (even though the bulb is on the bottom). You could lay one of those across the top of your x-ray to light it up from behind while its being scanned. Or you can figure out another way to evenly light up your x-ray from behind while your scanning it.
3try scanning them with the lid open. – Journeyman Geek – 2011-09-28T00:32:45.683
+1: I hope this works for transparencies too ... – Everyone – 2012-01-14T10:49:26.800