BD makes LRF and other formats using the book title as the file title. Most of the time this is fine. However, if you have already made a book with that title then it will be over-written.
This is easy to do because some titles are very common. Lots of works are titled, "Short Stories"; "Poems"; "Collected Poems".
So if you've used the title before then alter the filename when making the book. You can do this in the "Make Sony Reader Book" pane; and in the IMP, LIT and other panes.