additional folder "Messages" after mail import

Hi, I imported the mail from an old system (10.6) into a 10.8 system via "Import Mailboxes ..." in Mail.app.

I choose "Apple Mail" in the "Import data from:" window and selected the main directory where all the mailboxes and their messages sat.

After a couple of hours, after importing, the structure seemed to be replicated on the newer system,

except that every mail folder containing messages also contains a folder "Messages" showing exactly the same messages

as in the folder above.

Since that's many thousands of messages in hundreds of folders deleting the respective Messages-folder is not feasible.

How can I solve this?

Thanks, Michael.