Ok this mystery is solved. It turns out if you have metadata for either Publisher or Series that is longer then the window in the conversion area that the fields will run off of the screen.
I had a book that fetched
Code:
Harmondsworth, Eng : Penguin Books in association with H. Hamilton, 1955.
as the publisher. This was too long for the line and caused the fields for all books to exceed the window. As soon as I edited this field shorter then all books looked fine again.
Out of the 1800+ books in my library that one book was the cause of the problem. Once I edited this one book the conversion windows were normal again.