I had the same problem, as did a friend of mine with a similar setup. After reading a lot of posts here, I first
deleted all my downloaded books,
uninstalled Kindle for PC and the Calibre Plug-ins (from Tools 4.0). I then
installed Kindle for PC ver 1.4.1, and then
downloaded the books from Amazon again. I then
installed the plug-ins from Tools 4.6, and everything is working fine again. My Calibre version is 0.8.16, and as long as things are working, I'm not going to "upgrade" any of the elements mentioned above. It is my understanding from reading posts here that K4PC versions above 1.4.1 alter the book file a bit and sometimes prevent the plug-ins used with Calibre from working.
To find 1.4.1 I did a Google search and eventually found it.
Good luck.