Calibre is the best. I only had to delete my configuration directory twice and then everything has been fine.
Many settings/preferences are stored in the configuraton directory. When you get it working (and I know that you will) make a copy periodically and then you can just copy it back to have everything the way you want it.
Also if you find the directory by theducks method (which is the easiest but I assumed your calibre was frozen) First exit calibre, delete directory and restart calibre and it should just make a new configuration directory