I haven't played with cold bluing much, so I'm not of much help. However you sounded like the bluing was going 'OK' with the exception that there was rust coming from some remaining pits :shrug: I'm just wondering if there was some contamination in those pits that are causing you problems.
As I understand bluing it's actually a 'controlled rust'. So if the steel wasn't totally clean in those pits you could have two different types of 'rust' going on that don't go hand in hand well.
Just a thought.