I would say water is probably your problem. Dark urine is your kidneys way of telling you that your damaging them. Drink more water, if your taking in 1.5+ gallons a day - try some cranberry juice/extract.
Actually it should become crystal clear within 2-3 hours. I wake up at 4:00 every morning and piss out dark yellow urine. I'm on the job by 5:00 and by 6:00 and about a gallon later I'm all clear agian for the rest of the day.
My goal is about 3-4 gallons ed. Just completely stop drink ANYTHING but water.
I'm taking fina now and if i dont drink enough water throughout the day my urine is dark...as long as i drink at least a gallon a day everything is all good