I finaly figured it out. It has to do with files I put into the DVD Content folder. I copied a backup copy of all of my project files and put them in the DVD contents folder. They are a duplicate copies but I have done this type of backup before and it worked just fine without displaying "Duplicate File Found" message.... Why Encore even cares what I put in the DVD Contents folder...Why I don't know? I should be able to put practicaly any file in the dvd contents folder. This should be pretty much dummy information as far a Encore is concerned. It doesn't make sense. Why it sends off flags I have no clue why? I certainly don't find this a user friendly feature if it Adobe has done this on purpose.
I left this up so any poor soul can have at least some knowlege base. I couldn't find any when I went through it.