Blame the Cloud Collections update in the PW2 firmware v5.4.2 -- until Amazon fixes this (if ever) all collections will show their archived members as well.
If you desire to do so, and have the patience/inclination, then jailbreak your Kindle and follow the directions here:
http://ixtab.tk/kindle-touch-images/PW2/README.txt to revert back to the 5.4.0 firmware. Since it does not have Cloud Collections, this should be fixed.
WARNING: This is going to require technical stuff, there is no packaged update, yet. The Kindle developers corner is working on it, I believe...