Free these poor Kubes from their plastic prisons!!!
I've got loose Sacul, Toy Fair Vader, and Uzay Blue Star and have to say its pretty nice having them mixed in with the other figures. It is cool to have a few carded versions for display as well, but think of the added hassle there. How long will the cards last? How will you protect them? What if there is a flaw in the card? How much extra space do you take up with cards?
I am sorry for your losses, but you've got a good attitude about it. Maybe just keep going the way you are - keep what you can carded and when the cards fail, you have a minty fresh loose fig ready for display. In the bright side, letting the bubble fall off keeps the card nice and clean if you want to keep it.