I prefer most ebooks in ragged right (unjustified) format. When I selected the disable justification checkbox in the Create Ebook/Page Layout tab, nothing was created. Looking at the debug.txt output, I noticed that a --dont-justify was being added to the ebook-convert command line. According to ebook-convert's help output, that option does not exist. Instead there is a --change-justification=option command. Using either original or left as the option worked to create a non-justified ebook. My preference was left as that overrides justification present in the original text as well as that generated prior the conversion process.
Hmmm... since that's my major nit, have to say that otherwise BookCreator is a great time saving tool.