Having this exact same problem. Everything seems to set up correctly, but then as soon as I reload, all of the icons are out of order, and my network icon is now my shortcut overlay, my my documents icon is now my desktop icon, and so on. It's basically destroyed all usability on my PC since all of the icons are wrong, and I'm getting pretty steamed about having paid for this program given how poorly it works. I've now spent two days trying to fix it to no avail.

Can we get some help on this?

I probably should have been more clear - I originally started having the problem using an .ip I'd downloaded that had worked fine for months. However because of the way the package builder is designed (ie, not for Win7, it's missing all kinds of stuff including libraries, and is has a ton of icons only used by XP and lower) it's still necessary to make tweaks to those sorts of packages after loading it up. It seems as though you can apply such changes and get them to stick, but never save or reload the changed version (or switch between other IPs without losing all of said changes), which is presumably what happened to me. Doing so apparently causes this mess with the icons randomly rearranging. In fact, I can't load any downloaded IPs at all now, they are completely blank; the only ones that work appear to be my own hand-made ones through the package builder.

Honestly, I love this program, but it's a buggy mess that seems to gut the registry, and requires a lot of tiptoeing around and unintuitive trial and error. I'm constantly astonished that Stardock keeps selling it this way. It really needs some work to justify a fee.