I may not be reproducing this correctly (since it's not failing for me). I have Icon package X loaded. When I open IP I see that set in the default view and inthe preview sub-tab. What do you see?
This one seems to have fixed itself. It was when I would click on a new package when 'Filter by Catagory' was set to Film Strip.
Only display where? On the desktop? In Windows Explorer?
Desktop, shortcut folders, they should be the package closed folder icon. In Win Explorer it seems to be random folders that should be the packaged closed folder icon. Here are Screenshots:


and

What icons or apps specifiacally? Are they "standard" apps that have an icon built for them in IP?
As stated above and seen in the screenshots, in WinExplorer. They seem to be random, most are suppposed to be the package's default closed folder. Also the folders for Fonts, Games, and Downloaded Program Files don't change at all.
System Settings don't save or implement, if customized.
Trying to replicate.
My guess, as a user, is that this is because with Vista 64 the 'Apply Settings' button that usually appears in the top right of the window whenever something is changed, seems to be MIA.
Thank you for trying to replicate these issues. Hopefully it'll lead to a fix of one sort or another, soon.
P.S. I was able to play with IP on my XP machine and there don't seem to be any issues. Yay that!