I was perusing the bug list and noticed that many people dont' think the upgrade works. They have the problem of trying to pull an item off and it "poping" back on unless they clear the whole thing. I upgarde my ships constantly (it rocks , all shipards currently producing the old version switch on their own) and don't have this problem and here is why.
The simple work around is when you open the screen up to upgarde your design and remove (via list or clicking dosn't matter) the item - RIGHT CLICK . Before you do anything else right after you have removed the first thing just right click in the 3d window.
I belive this bug is actually a failure of the program to "deselect" the item after you remove it. So then when you go to do something else having not right clicked (which deselects anything in focus) the program hasn't actually finished removing the item. So anytime you have a problem with a part "poping" back on just right click in the 3d window after you remove it.
P.S. There is another bug in this window that relates to parts. When you have a list of parts that forces you to scroll to get to the end of it. If scroll and then remove a part the part picture dosn't leave the scroll bar. The part is gone and if you scroll left it disapears after it's off screen and corrects itself. I dunno if this is related to the above someone more industrious than I can do some testing thow.