I'm having a little bit of trouble with my Kobo and Calibre too. Using Calibre I've converted from PDB and PDF files to EPUB but the font sizes are stuck at really small and nothing I can do will fix that (using the base font size didn't do anything). I think I'll try the KoboBulkFixer mentioned and hope that the firmware fix helps. I would like to see this capability in Calibre so that I can use one program to do everything
In addition, I downloaded the correct covers for the books when they'd been converted to EPUB (I downloaded the covers and converted them again) but they're while they're showing up on Calibre, they're not doing so on the Kobo.