Stains in your chamois, all the years that I have cycled, I have never had any stains that will not wash out regardless of what powder that I use (Even checked all my shorts just now), but end of day does it matter, no one will see them unless you wear them inside out.
But aside from that one thing that I always do is, wash them as normal with minimum powder along with all my cycling clothes and then give them all another rinse to ensure no trace of detergents etc are left. Nothing no worse on a hot sweaty day when you start itching caused by any residue detergent reacting with sweat, it can drive you bonkers.