I am not sure if this is a bug or a structural issues. I tried to find other incidents on the help and net to no avail. It may be a drag and drop issue as I did mess around with the surveys initial order and their is some mention of drag and drop messing the logic up.
After moving the order around the questions I then changed two questions (#3 and #4) from a radio button box to a ranking grid. As the logic needed to be updated I removed the existing logic and when I tried to add new logic to the 4th and 5th questions ( an existing check box type). Both now will only offer questions 1 and 2 as logic options, not question 3 which is the one needed.
Problem Solved. Was in the directions all along. You cannot use a Rank Grid question to drive the logic of other questions.