I can't stand how Closet Gnome automatically opens up all the Blizzard default bags whenever I try to Add/edit a set. And then it leaves open the main backpack when you are done. Really annoying. Especially if you use something like Baggins' or Onebag and don't use the default bags.
I'm having the exact same issue.
One thing I miss from ItemRack is the ability to assign icons to a set. Being able to tell at-a-glance which set you have equipped is nice.
Control Click on one of the items that you have defined for a set to set it as the set icon. Okay, I said set a lot in there. I think you can do it for any icon on your character frame, so it doesn't necessarily need to be in the set. I have only tried with equipped items in the set however.