throttleman,
If I read you correctly, The rust is coming from the hot, soapy water and rinse cycles. Using an alcohol rinse/patch (use the 90% drugstore variety) after the water rinse, will clear any water left behind.
The steel used in these muzzle loaders is definately the reason for the quick rusting so get it dried PRONTO...then use Ballistol or good penetrating oil like previously mentioned as a last step. Finally, stand your barrel muzzle down to make certain you don't get any water sitting in the breech.
Jim