Great tool ! Rated 4 out of 5 stars

Worked very well for me on all basic tasks. Nevertheless, I've had to import a very large mail structure (lots of folders and mails), and the ImportTool kept showing me "Do you want to import...... [folder_path\folder]?". It had like 300 folders so it's been looooooong !! I'd suggest adding a "Yes to all" or "Import all" feature !
Congrats again and bye.

This review is for a previous version of the add-on (2.6.1). 

That option exists!

If I've understood well your situation, go at Tools --> ImportExportTools --> Options and uncheck the preference "Ask confirm before importing mbox files from a directory".