Have tried backspacing to the final full point at the end of chapters to remove any spurious characters. Tried all variations in “Separators”. Seems to occur whether between folders, folders to text files or text files to folders. Any ideas?
Look at your Compile options and make sure Page Break Before is not checked.
This is a bug. I have posted the steps to reproduce this in the Bug forum.
Same bug when compiling to .epub. I posted in Bug section.