Can you track the rogue pixels down in the raw images? If it is in every image then it should have been in the master dark and corrected but you could add it to the cosmetic file and zap it that way.
I dont know about BASS but the ISIS cosmics removal tool works on the individual sub exposures where a rogue pixel stands out more clearly than in the combined spectrum image. It compares each pixel with its neighbours, looking at the differential between each pixel and the surrounding ones. You can set the threshold so if a pixel is poking its head above its neighbours, ISIS will zap it. (If you set it too low though, particularly if the spectrum is close to undersampled, it can zap a whole row or spectrum line so you have to use it with caution)