Just a few thoughts:
Before applying the brown, did you soak the entire barrel with a reputable de-greaser, such as Gunscrubber, and then wipe it down several times, to remove absolutly all grease and oil?
Is it possible that in those two areas, you previously spilled a little Lokt-Tight or other similar enamel, that filled the pores of the metal and is still present? (You would need to research to find a proper solvent. Acetone perhaps?)
Is it possible that on those two bad areas, you used a different grade of sandpaper than you used on the rest of the barrel, or that you didn't sand it as much as the rest of the barrel?
I think that I would try the spot repair approach before I re-did the whole barrel. Sand those areas back down to the bare metal, apply lots of degreaser, maybe some acetone, make sure it is totally dry, and then try again.