I finally got it working (had a slight issue where it was showing in the top menubar on my mac, then disappeared when I plugged the Kindle in, I added it to every menu I could see in the preferences and bingo!). I set up my collections, told it to sync, restarted my kindle and there were the collections! They were empty but I noticed the spinning wheel (top right corner) and after a few minutes my collections were full!
I officially love you! Now I just have to get the Meta Plugboards working how I want and I'll be a super happy bunny