WD40 when used as water displacement is fine for muzzle loaders. WD40 is not fine when used as a rust inhibitor. Use Barricade or G96 as a rust inhibitor.Thanks all for the suggestions, I read somewhere once that WD40 was bad is muzzleloaders but enough people here are using it maybe it's worth a try. Pretty sure I have a full can in the shed.
I'm still not sure what I've done to create the flash rust, the water I used last night by the end was room temp if not on the cold side.
Local water can have some chemicals such as chlorine that can lead to flash rust. The WD40 will also pull out the chemicals along with the water.