Well the new firmware update for the A&R software (the Borders one too, which I agree is terrible, it hangs a lot too) should be out soon (according to http://blog.kobobooks.com/
) but I'm currently not rushing for it because I like the idea of the cover being on my Kobo.
As for the font problem you might be able to run it though the font fixer at http://www.mobileread.com/forums/showthread.php?t=83209
I've used this and its fixed most of the font resize problems that I have had when using books.
Calibre is good for non-DRMed books but when you are using DRMed books it doesn't work as well, but IMHO its 100x better than the Border's software for constructing your library (and doesn't fill up the "I'm reading" list)