We had the same problem in a house we purchased and the most stains were where the sun came thru the front door window. I tried all that you did and then finally gave up until one day I poured a lot of baking soda on all the stains and let it sit for a day or two and it worked. No more odors!! It was an inconvenience for a few days with the baking soda all over the underlayment, but it worked and cleaned up rather well! Good Luck!!