Ok spotted one bug related to supporting .MOBI extensions. On a reload of the .MOBI file the Book Title text does not reflect the Title contents stored in the .MOBI file it still reports the Database name.
Because the GUI originally only supported PRCs I grabbed the Database name and automatically write that out as the Book Title. If you don't specify a --Title flag when converting, I found that the Title contents reflected the pathname of the original file, which would look weird in Mobipocket etc that refer to the Title field. (Must report this as a bug to tompe actually)