[bpalesch]

OK, so here's how the Collections plug in seems to work properly:

1. Open Calibre.
2. Connect Kindle.
3. Upload any books.
4. Click, "Create collections on the Kindle from Calibre.
5. Wait until told to eject device and do so.
6. Restart Kindle.

At this point when the Kindle comes back on, you may see everything REMOVED from collections. If so, add the following steps:

7. Kill a chicken and dribble its blood on the ground while reciting the Jabberwocky.
8. Close Calibre.
9. Restart Calibre.
10.Repeat steps 1. through 6. above.

Running it twice is a pain in the butt, but takes less time than adding each book to a collection on the Kindle manually.