which stage of the A/B are you talkin about? if its in the beginning where youve initially basified and tossed in the NP then probably not, most of the goods should transfer over to the nonpolar layer... UTFSE for info on clearing emulsions  

That white clumpy stuff is your basifyed pseudo If you look closer it is in the bottom of the top layer...

Ok, well I added dh2o to the NP then added Muriatic acid till ph6, the water became cloudy but most of the gump stayed where it was, does this sound right, sorry for the questions that I am sure seem stupid to the more experienced.

What white clumpy stuff?

If we knew the pills you were extracting from and what you did to the pill mass before attempting the a/b, or if we knew how you did the a/b, we might have some clue as to whether the white clumpy stuff was anything to worry with or not. I've seen a few more types of white clumpy stuff at the interface than one. Most of them were not something I cared to keep. A couple of times they were.

My point is that without knowing what you were extracting from and the method you used to extract, all we can do is guess.