I thought that the upper phase was some kind of buffer as well. However, I looked at the MSDS and it said that there was phenol, ChCl3, and IAA. It did not mention anything else, like Tris. So I was suspicious the upper phase was something useful to the extraction.
pGL3 has relatively high background activity which can be inducible upon stimulation with exogenous agents. I think its because of some kind of cryptic promoter activity. I know that pXPG-Luc has lower background activity (like 20 x lower than pGL3 Basic in HEK293 T) but also I strongly suspect the new version pGL4 Basic is better as well. pXPG is avaialble from Peter Cockerill and pGL4 from Promega.