I had this happen on a batch of IPA over the summer. I dry hopped it longer than I wanted to, but other than that, no real production issues. I cold crashed and kegged it around the first of October, and bottled off a couple of 12 packs to share with people. They tasted great, but had that same sort of muddy brown color, but I chalked it up to not being totally settled yet. However, over the next few weeks they got worse. They lost the fruity hop flavor and were kind of muddled. I also discovered around this time that I had a regulator leak, and that my beer in the bottles was under carbonated, which I thought was the reasoning. I just left the beer in the fridge for a while.
Fast forward to a week or two ago. I popped another bottle. What a change! The color is a beautiful hazy orange, and it has an incredible tropical fruit flavor again.
What causes this? No idea. For being cold crashed, and bottled from a keg, there's a pretty considerable amount of sediment in the bottles though. Maybe the yeast were still doing some work. Maybe it's just cold conditioning doing some good. Some yeast can do biotransformations of hop components. I don't know enough about that to really comment though.
