Have been experimenting with my new Kindle3 3g EU with v3.2.1 firmware on which I have the full version of Duokan, Jailbreak 3.2.1, Launchpad and Font hacks.
I am running Win7 x64 and can report that Kindleabra works fine for me and have successfully created, deleted Collections and moved books around between them. All changes look correct after a reboot.
I have also tried KKCM, but although the scripts run (apparently correctly) these programs did not organise my Collections correctly. Not sure what I haven't done.