Why or what would cause an amethyst to become discolored?
Some amethyst can fade to a lighter color upon prolonged exposure to light. If that's the case it is not unusual. Is that the discoloration that you experienced?
quite the opposite, I had it stored in a box, there is not direct sunlight and the room tends to be really cold.
That is odd - never heard of discoloration in amethyst other then light exposure. If anyone else has any similar experiment please share.
Most citrine sold in this country is heat-treated amethyst, which turns yellow-brown when exposed to heat.
Eeven though the amethyst was in a box it can still attract negative energy.
You need to cleanse the stone; if possible bury it for 24 hrs (or longer) in "clean" soil.