Where on your Kobo ereader's exposed storage are you placing the books? When you reconnect your Kobo to your Mac, are you able to browse the exposed storage and see the ebooks? Placing them in the root of the exposed storage is not recommended since the number of directory entries is limited. Create a directory (I use eBooks) to store them. In the KoboTouch or KoboTouchExtended driver, I use the following save template :
Code:
eBooks/{author_sort:sublist(0,1,&)}/{title} - {authors:sublist(0,1,&)}
So basically, store the books in eBooks in a directory created from the first author sort value for the book with the filename created from the title and the first author name. i.e. eBooks/Flint, Eric/Mother of Demons - Eric Flint.epub
Limiting to the first author sort/author is simply to keep the file paths and names shorter.
Another item to try is to remove the two calibre files in the root of the exposed storage (driveinfo.calibre & metadata.calibre), safely ejecting, reconnecting and seeing if calibre recreates them when you connect.
Does Kobo Utilities report your database as being ok? Kobo Utilites => Database => Check the device database.