I imported the pdf back in, and I get a box that opens asking me at what dpi I want the transparency?... I have never been asked that question before and I know the file technically should have no transparencies in it. Once I tell it how much dpi I guess it converts the entire file into a bitmap, and I have no choice but to tell it a dpi, so there seems no way around it.
Now in Flexi I can bring the file in and I can break the masks down... although for what should be a simple file there were about 4 or 5 of them. Once they are all broken down and deleted the file is fine..... I can alter and do what i please.
I find that as time goes on I am experiencing more and more strange attributes to files and trying to deal with them can be quite trying.