Paint.NET :: Semi-transparency And Clone Stamp

I tried searching things like "semi-transparency" and "clone stamp", but was unable to turn up any search results relevant.

Essentially, the problem is that I have a semi-transparent image, and I need to clone some of that image and graft it onto the same image. Unfortunately, when I use the clone stamp, it doesn't seem to properly copy the transparency.

Here is the image in question: [URL] ...........

(Actually, this isn't the REAL image in question - the real image is actually a .dds file, a texture - an inventory screen in particular - for a game I'm trying to edit. Not sure if that makes a difference.)

As you can see, (most of) the (insides of the) boxes are semi-transparent. What I'm trying to do is somewhat extend the very bottom left box to be exactly 33% wider, and also somewhat extend the very bottom right box, (how much, haven't figured out). Those are where items would normally be located, but unfortunately, they are sometimes not big enough for a particular item or particular amount of items that I'm trying to fit in them and they both need to be a little bit longer. However, I am no artist. What I thought I'd try to do was use the clone stamp on them to simply extend them, (and cover up any obvious duplication). But when I attempt to use the clone stamp, all the transparency goes away and I'm left with solid colors, which is not good. I tried using Photoshop to do this, but Photoshop has no official support for texture files and the available plugin for them does not handle transparency correctly and screws up the entire thing as well, even if it looks correct while editing it. I also tried using GIMP, but GIMP doesn't...do something correctly, (what's wrong, I can't remember - doesn't matter). Paint.net displays exactly what you see in game, but unfortunately I can't figure out how to use the proper tools to actually edit it to my needs.