I am not entirely sure what is going on, but I have had all of my Item Sets deleted twice now. I'm not going to rage about this, but I did put a good amount of time in putting them together. I just want to know if there is any particular reason that this has happened? I don't feel inclined to take advantage of the feature because I do not know if all the sets will be deleted again.
Item sets are stored in your local user preferences. So if you change machines or reinstall you will have to rebuild them. It's a little less than ideal, sorry. As a workaround, you can copy your preferences file to the new location if you've invested a lot of effort in them. I'd like to have a better solution for this problem.