Say no more my friend, thats the exact problem I had. I was able to clear my problem up however. The dealer can reflash, but it only works periodically for me. A guy with toyo corporate recommended that I run some e85 to help show my truck the difference between regular fuel and e85 since this problem is created from the truck thinking it has e85 in the tank and running rich, while not actually having e85 in the tank. I ran one take of e85, got absolutely HORRIBLE gas mileage, then ran some true 100% gasoline and it seems to have fixed the issue for now. May wanna try that.
The problem is the truck is reading an incorrect perceived alcohol density, thus running in e85 and doing stupid crap.